Taxonomy of protists

A protist (/ˈproʊtɪst/) is any eukaryotic organism (one with cells containing a nucleus) that is not an animal, plant, or fungus. The protists do not form a natural group, or clade, since they exclude certain eukaryotes with whom they share a common ancestor;^[a] but, like algae or invertebrates, the grouping is used for convenience. In some systems of biological classification, such as the popular five-kingdom scheme proposed by Robert Whittaker in 1969, the protists make up a kingdom called Protista, composed of "organisms which are unicellular or unicellular-colonial and which form no tissues".^[1][b] In the 21st century, the classification shifted toward a two-kingdom system of protists: Chromista (containing the chromalveolate, rhizarian and hacrobian groups) and Protozoa (containing excavates and all protists more closely related to animals and fungi).^[2]

A modern non-hierarchical interpretation of the phylogeny of eukaryotes, including protists
(the gray unlabeled line next to Sar represents Telonemia)

The following groups contain protists. The clade Opisthokonta also contains the animals and the fungi, and the kingdom Archaeplastida also contains algae and plants.

Symbols and abbreviations used:

nom. cons. — Indicates a conserved name, a name which has been chosen for a taxon despite not being the priority name.

ICZN/ICN — Indicates an ambiregnal taxon that is accepted in both the zoological and the botanical codes of nomenclature, regulated by the ICZN and the ICN respectively.

(P) — Indicates a paraphyletic taxon.

† — Indicates an extinct taxon.

? — Indicates a taxon of uncertain taxonomic position, which may be the case for various reasons, including a lack of genetic data.

→ — Indicates a monotypic relationship.

Current classification

This article largely follows the efforts of the scientific community and the International Society of Protistologists to revise the taxonomy of protists in a manner that reflects their phylogeny and evolution, striving away from the use of historical paraphyletic taxa and relying exclusively on clades as the basis of the classification. The reference used for the general arrangement of groups is the publication Revisions to the Classification, Nomenclature and Diversity of Eukaryotes, published in 2019 by researcher Sina Adl and coauthors.^[3] Other studies are used for some specific groups of protists that have been revised after 2018, such as slime moulds,^[4] glaucophyte algae,^[5] arcellinid testate amoebae^[6] and planktonic foraminifera.^[7] The usage of higher-level taxon ranks (phylum and kingdom) is unstable, as it varies from one author to the next;^[8][9] as such, said ranks are generally omitted.

The following cladogram shows the relationships between the major groups of protists, as well as the kingdoms of animals, plants and fungi, according to the most recent phylogenetic analyses.^{[10][11][12][13][14][15]}

Eukaryota	Diaphoretickes TSAR SAR Halvaria Stramenopiles Alveolata Rhizaria Telonemia Haptista CAM Cryptista Microheliella Archaeplastida (Kingdom Plantae s.l.) Provora Hemimastigophora Meteora sporadica Discoba Jakobea Tsukubea Discicristata Heterolobosea Euglenozoa Metamonada Malawimonada Ancyromonadida Podiata CRuMs Amorphea Amoebozoa Obazoa Breviatea Apusomonadida Opisthokonta Holomycota Fungi Cristidiscoidea Holozoa Ichthyosporea Pluriformea Tunicaraptor Filozoa Filasterea Choanozoa Choanoflagellata Metazoa (Kingdom Animalia)	Choanozoa (P) sensu Cavalier-Smith Excavates (P)

Amorphea .mw-parser-output .nobold{font-weight:normal}Adl et al. 2012

Obazoa Brown et al. 2013

Breviatea Apusomonadida Opisthokonta Nucletmycea Fungi 'True fungi' Aphelida Rozellida Microsporidia Rotosphaerida Holozoa Ichthyosporea Dermocystida Ichthyophonida Pluriformea Corallochytrium Syssomonas Filozoa Filasterea Choanozoa Choanoflagellata Metazoa

Cladogram of Obazoa based on several analyses.[13][16] It includes the earliest diverging 'fungi' (microsporidians, aphelids and rozellids), which are only sometimes considered protists under the name of Opisthosporidia.[17]

• Class Thecomonadea^[c] Cavalier-Smith 1993 emend. 2013 → order Apusomonadida Karpov & Mylnikov 1989 → family Apusomonadidae Karpov & Mylnikov 1989. Genera not assigned to a subfamily: Amastigomonas de Saedeleer 1931; Multimonas Cavalier-Smith 2010; Podomonas Cavalier-Smith 2010; Catacumbia Torruella, Galindo et al. 2022; Cavaliersmithia Torruella, Galindo et al. 2022.^[19]
  • Subfamily Apusomonadinae Cavalier-Smith 2010. Genera: Apusomonas Aléxéieff 1924 (=Rostromonas Karpoff & Zhukov 1980); Manchomonas Cavalier-Smith 2010.
  • Subfamily Thecamonadinae Larsen & Patterson 1990. Genera: Chelonemonas Heiss, Lee, Ishida & Simpson 2015; Karpovia Torruella, Galindo et al. 2022; Singekia Torruella, Galindo et al. 2022, Thecamonas Larsen & Patterson 1990.
• Class Breviatea^[c] Cavalier-Smith 2004 → order Breviatida Cavalier-Smith 2004 → family Breviatidae Cavalier-Smith 2013. Genera: Breviata Walker, Dacks & Embley 2006; Lenisia Hamann et al. 2016; Pygsuia Brown et al. 2013; Subulatomonas Katz et al. 2011.

Opisthokonta Cavalier-Smith 1987 emend. Adl et al. 2005

• Nucletmycea Brown et al. 2009 (=Holomycota Liu et al. 2009)
  • Order Rotosphaerida Rainer 1968 (=Cristidiscoidida Page 1987) → family Nucleariidae Cann & Page 1979 (=Pompholyxophridae Page 1987). Genera: Fonticula Worley, Raper & Hohl 1979; Nuclearia Cienkowsky 1865; Parvularia López-Escardó & Torruella 2017; Pompholyxophrys Archer 1869; Lithocolla Schulze 1874; Vampyrellidium^? Zopf 1885; Elaeorhanis^? Greeff 1873; Pinaciophora^? Greeff 1869; Rabdiophrys^? Rainer 1968; Rabdiaster^? Mikrjukov 1999; Thomseniophora^? Nicholls 2013.^[20]
  • Kingdom Fungi R.T. Moore 1980. Excluded from protists.
• Holozoa Lang et al. 2002. Incertae sedis genera: Tunicaraptor Tikhonenkov, Mikhailov, Hehenberger, Karpov, Prokina, Esaulov, Belyakova, Mazei, Mylnikov, Aleoshin & Keeling 2020;^[13] †Bicellum Strother & Wellman 2021.^[21]
  • Class Ichthyosporea^[d] Cavalier-Smith 1998 (=Mesomycetozoea Mendoza et al. 2002)
    • Order Dermocystida Cavalier-Smith 1998 → family Rhinosporidaceae Mendoza et al. 2001. Genera: Amphibiocystidium Pascolini et al. 2003; Amphibiothecum Feldman, Wimsatt & Green 2005; Chromosphaera Grau-Bové et al. 2017; Dermocystidium Pérez 1908; Rhinosporidium Minchin & Fantham 1905; Sphaerothecum Arkush et al. 2003, Valentines Borteiro et al. 2018.^[22]
    • Order Ichthyophonida Cavalier-Smith 1998 (=Ichthyophonae Mendoza et al. 2001) → family Amoebidiidae Reeves 2003. Genera: Abeoforma, Amoebidium, Anurofeca, Astreptonema, Caullerya, Creolimax, Eccrinidus, Enterobryus, Enteropogon, Ichthyophonus, Palavascia, Pseudoperkinsus, Psorospermium, Sphaeroforma.
  • Class Pluriformea^[d] Hehenberger et al. 2017 → order Corallochytrida Cavalier-Smith 1995 emend. 2021^[18]
    • Family Corallochytriidae Cavalier-Smith in Cavalier-Smith & Allsopp 1996. Sole genus: Corallochytrium Raghu-Kumar 1987.
    • Family Syssomonadidae Cavalier-Smith 2021.^[18] Sole genus: Syssomonas Tikhonenkov, Hehenberger, Mylnikov & Keeling 2017.
  • Class Filasterea Shalchian-Tabrizi et al. 2008 → order Ministeriida Cavalier-Smith 1997. Genus not assigned to families: Pigoraptor Tikhonenkov, Hehenberger, Mylnikov & Keeling 2017.
    • Family Ministeriidae Cavalier-Smith 1997. Sole genus: Ministeria Patterson et al. 1993.
    • Family Capsasporidae Cavalier-Smith 1997. Sole genus: Capsaspora Hertel et al. 2002.
    • Family Txikisporidae Urrutia, Feist & Bass 2022. Sole genus: Txikispora Urrutia, Feist & Bass 2022.^[23]
  • Choanozoa Brunet & King 2017^[e]
    • Class Choanoflagellata Kent 1880–1882 (=Craspedomonadina Stein 1878, Craspedomonadaceae Senn 1900, Craspedophyceae Chadefaud 1960, Craspédomonadophycidées Bourrelly 1968, Craspedomonadophyceae Hibberd 1976, Choanomonadea Krylov et al. 1980, Choanoflagelliida Lee, Hutner & Bovee 1985, Choanoflagellatea Cavalier-Smith 1997 emend. Cavalier-Smith 1998, Choanomonada Adl et al. 2005)^[24][25]
      • Order Craspedida Cavalier-Smith 1997, emend. Nitsche et al. 2011 → family Salpingoecidae Kent 1880–1882, emend. sensu Nitsche et al. 2011 (=Codonosigidae Kent 1880–1882). Genera: Astrosiga Kent 1878; Aulomonas Lackey 1942; Barroeca Hake, Burkhardt, Richter & King 2024;^[26] Choanoeca Ellis 1930, Cladospongia M.O.P.Iyengar & K.R.Ramanathan 1940; Codonocladium Stein 1878; Codonosigopsis Senn 1900, Codosiga James-Clark 1866 (=Codonosiga Stein 1878); Desmarella Kent 1878 (=Codonodesmus Stein 1878, Kentrosiga Schiller 1953); Dicraspedella Ellis 1930; Diploeca Ellis 1930; Diplosiga Frenzel 1892; Diplosigopsis Francé 1897; Hartaetosiga Carr, Richter & Nitsche 2017; Kentia Schiller 1953; Lagenoeca Kent 1881; Microstomoeca Carr, Richter & Nitsche 2017; Monosiga Kent 1878; Mylnosiga Carr, Richter & Nitsche 2017; Pachysoeca Ellis 1930; Proterospongia Kent 1882; Salpingoeca James-Clark 1866; Salpingorhiza Klug 1936; Sphaeroeca Lauterborn 1894; Stagondoeca Carr, Richter & Nitsche 2017; Stelexomonas Lackey 1942; Stylochromonas Lackey 1940.
      • Order Acanthoecida Cavalier-Smith 1997, emend. Nitsche et al. 2011
        • Family Acanthoecidae Norris 1965, emend. sensu Nitsche et al. 2011. Genera: Acanthoeca Ellis 1930; Enibas Schiwitza, Arndt & Nitsche 2019;^[27] Helgoeca Leadbeater 2008; Polyoeca Kent 1880; Savillea Loeblich 1967.
        • Family Stephanoecidae Leadbeater 2011. Genera: Acanthocorbis Hara & Takahashi 1984; Amoenoscopa Hara & Takahashi 1987; Apheloecion Thomsen in Thomsen & Boonruang 1983; Bicosta Leadbeater 1978; Calliacantha Leadbeater 1978; Calotheca Thomsen & Moestrup 1983; Campanoeca Throndsen 1974; Campyloacantha Hara & Takahashi 1987; Conion Thomsen 1982; Cosmoeca Thomsen 1984; Crinolina Thomsen 1976; Crucispina Espeland in Espeland & Throndsen 1986; Diaphanoeca Ellis 1929; Didymoeca Doweld 2003; Kakoeca Buck & Marchant in Buck et al. 1990; Monocosta Thomsen 1979; Nannoeca Thomsen 1988; Parvicorbicula Deflandre 1960; Platypleura Thomsen 1983; Pleurasiga Schiller 1925; Polyfibula Manton in Manton & Bremer 1981; Saepicula Leadbeater 1980; Saroeca Thomsen 1979; Spinoeca Thomsen in Thomsen, Østergaard & Hansen 1995; Spiraloecion Marchant & Perrin 1986; Stephanacantha Thomsen in Thomsen & Boonruang 1983; Stephanoeca Ellis 1930; Syndetophyllum Thomsen & Moestrup 1984.
    • Kingdom Metazoa Haeckel 1874, emend. Adl et al. 2005 (=Animalia Linnaeus 1758). Excluded from protists.

Phylum Amoebozoa Lühe 1913, sensu Cavalier-Smith 1998

Tubulinea Corycida Echinamoebida Elardia Leptomyxida Euamoebida Arcellinida Discosea Centramoebia Acanthamoebida Pellitida Himatismenida Flabellinia Dermamoebida Vannellida Dactylopodida Thecamoebida Stygamoebida Evosea Cutosea Conosa Variosea Cavosteliida Fractovitelliida Profiliida Archamoebea Eumycetozoa Dictyostelia Protosporangiida Myxogastria

Cladogram of Amoebozoa based on an 824-gene phylogenetic analysis published in 2022.[28]

• Incertae sedis genera: Belonocystis; Boveella; Biomyxa; Corallomyxa; Gibbodiscus; Hartmannia; Malamoeba; Malpighamoeba; Oscillosignum; Pseudothecamoeba; Rhabdamoeba; Schoutedamoeba; Stereomyxa; Subulamoeba; Triaenamoeba; Unda.^[3]

Class Tubulinea Smirnov et al. 2005

• Corycidia Kang et al. 2017^[29]
  • Order Trichosida Möbius 1889 → family Trichosphaeriidae Sheehan & Banner 1973 (=Trichosidae Möbius 1889). Sole genus: Trichosphaerium Schneider 1878 (=Atrichosa Cavalier-Smith et al. 2016).
  • Family Microcoryciidae de Saedeleer 1934. Genera: Amphizonella Greeff 1866; Diplochlamys Greeff 1888; Microcorycia^? Cockerell 1911; Parmulina^? Penard 1902 emend. 1909; Penardochlamys^? Deflandre 1953; Zonomyxa^? Nusslin 1882.^[f]
• Subclass Echinamoebia Cavalier-Smith et al. 2016 → order Echinamoebida Cavalier-Smith et al. 2004 emend. Smirnov et al. 2011
  • Family Echinamoebidae Page 1975. Genera: Echinamoeba Page 1975; Micriamoeba Atlan et al. 2012.
  • Family Vermamoebidae Cavalier-Smith & Smirnov 2011. Sole genus: Vermamoeba Cavalier-Smith & Smirnov 2011.
• Elardia Kang et al. 2017^[29]
  • Subclass Leptomyxia Cavalier-Smith et al. 2016 → order Leptomyxida Pussard & Pons 1976 emend. Page 1987
    • Family Leptomyxidae Pussard & Pons 1976. Sole genus: Leptomyxa Goodey 1915 emend. Smirnov et al. 2017.
    • Family Rhizamoebidae Smirnov et al. 2016. Sole genus: Rhizamoeba Page 1972 emend. Smirnov et al. 2017.^[30]
    • Family Flabellulidae Bovee 1970. Sole genus: Flabellula Schaeffer 1926 emend. Tyml, Lisnerová, Kostka & Dyková 2018^[31] (includes Paraflabellula Page & Willumsen 1983).
    • Family Gephyramoebidae Pussard & Pons 1976. Sole genus: Gephyramoeba Goodey 1915.^[30]
  • Superorder Eulobosia Cavalier-Smith et al. 2016
    • Order Arcellinida Kent 1880. Incertae sedis genera: Acipyxis Jung 1942; Apolimia Korganova 1987; Argynnia Vucetich 1974; Armipyxis Dekhtjar 2009; Conicocassis Nasser & Patterson 2015; Cornuapyxis Coûteaux & Chardez 1981; Ellipsopyxella Bonnet 1975; Ellipsopyxis Bonnet 1975; Erugomicula Nasser et al. 2021; Frenopyxis Bobrov & Mazei 2020; Geamphorella Bonnet 1959; Geoplagiopyxis Chardez 1960; Geopyxella Bonnet & Thomas 1955; Hoogenraadia Gauthier-Liévre & Thomas 1958; Jungia Loeblich & Tappan 1961; Lagenodifflugia Medioli & Scott 1983; Lamptopyxis Bonnet 1974; Lamtoquadrula Bonnet 1975; Leptochlamys West 1901; Maghrebia Gauthier-Liévre & Thomas 1958; Meisterfeldia Bobrov 2016; Microquadrula Golemansky 1968; Nabranella Snegovaya & Alekperov 2009; Oopyxis Jung 1942; Paracentropyxis Bonnet 1960; Paraquadrula Deflandre 1932; Pentagonia Gauthier-Liévre & Thomas 1958; Physochila Jung 1942; Planhoogenraadia Bonnet 1977; Pomoriella Golemansky 1970; Pontigulasia Rhumbler 1895; Prantlitina Vašíček & Růžička 1957;^[32] Proplagiopyxis Schönborn 1964; Protoplagiopyxis Bonnet 1962; Protocucurbitella Gauthier-Liévre & Thomas 1960; Pseudawerintzewia Bonnet 1959; Pseudonebela Gauthier-Liévre & Thomas 1953; Schoenbornia Decloître 1964; Sexangularia Awerintzew 1906; Suiadifflugia Green 1975; Trigonopyxis Penard 1912; Wailesella Deflandre 1928;^[6] †Cangwuella K.Wang et al. 2024.^[33]
      • Suborder Phryganellina Bovee 1985
        • Family Phryganellidae Jung 1942. Sole genus: Phryganella Penard 1902.
        • Family Cryptodifflugiidae Jung 1942. Sole genus: Cryptodifflugia Penard 1890.^[34]
      • Suborder Organoconcha Lahr et al. 2019 → family Microchlamyiidae Ogden 1985. Genera: Microchlamys Cockerell 1911 (=Pseudochlamys Claparède & Lachmann 1859); Spumochlamys Kudryavtsev & Hausmann 2007; Pyxidicula Ehrenberg 1838.
      • Suborder Glutinoconcha Lahr et al. 2019
        • Infraorder Volnustoma Lahr et al. 2019 → family Heleoperidae Jung 1942. Genera: Heleopera Leidy 1879; Metaheleopera^? Bartoš 1963.
        • Infraorder Hyalospheniformes Lahr et al. 2019 → family Hyalospheniidae Schultze 1877 emend. Kosakyan et al. 2012. Genera: Alabasta Duckert, Blandenier, Kosakyan & Singer 2018; Alocodera Jung 1942; Apodera Loeblich & Tappan 1961; Certesella Loeblich & Tappan; Cornutheca Kosakyan, Lahr, Mulot, Meisterfeld, Mitchell & Lara 2016; Gibbocarina Kosakyan, Lahr, Mulot, Meisterfeld, Mitchell & Lara 2016; Hyalosphenia (Stein 1857) Schulze 1877; Longinebela Kosakyan, Lahr, Mulot, Meisterfeld, Mitchell & Lara 2016; Mrabella Kosakyan, Lahr, Mulot, Meisterfeld, Mitchell & Lara 2016; Nebela Leidy 1874 emend. Kosakyan, Lahr, Mulot, Meisterfeld, Mitchell & Lara 2016; Padaungiella Lara & Todorov 2012; Planocarina Kosakyan, Lahr, Mulot, Meisterfeld, Mitchell & Lara 2016; Porosia Jung 1942 emend. Bobrov & Kosakyan 2015; Quadrulella Cockerell 1909 emend. Kosakyan, Lahr, Mulot, Meisterfeld, Mitchell & Lara 2016.
        • Infraorder Excentrostoma Lahr et al. 2019 → family Centropyxidae Jung 1942 (includes Plagiopyxidae Bonnet & Thomas 1960). Genera: Awerinzewia Schouteden 1906; Bullinularia Deflandre 1953; Centropyxis Stein 1859; Frenopyxis Bobrov & Mazei 2020;^[35] Golemanskia González-Miguéns, Todorov, Blandenier, Porfirio-Sousa, Ribeiro, Ramos, Lahr & Lara 2022;^[6] Plagiopyxis Penard 1910.
        • Infraorder Cylindrothecina González-Miguéns, Todorov, Blandenier, Porfirio-Sousa, Ribeiro, Ramos, Lahr & Lara 2022 → family Cylindrifflugiidae González-Miguéns, Todorov, Blandenier, Porfirio-Sousa, Ribeiro, Ramos, Lahr & Lara 2022. Sole genus: Cylindrifflugia González-Miguéns, Todorov, Blandenier, Porfirio-Sousa, Ribeiro, Ramos, Lahr & Lara 2022.^[6]
        • Infraorder Longithecina Lahr et al. 2019
          • Family Difflugiidae Wallich 1864. Genera: Difflugia Leclerc 1815, Zivkovicia Ogden 1983.
          • Family Lesquereusiidae Jung 1942. Sole genus: Lesquereusia Schlumberger 1845.
        • Infraorder Sphaerothecina Kosakyan, Lara & Lahr 2016
          • Family Arcellidae Ehrenberg 1843. Genera: Arcella Ehrenberg 1830; Galeripora González-Miguéns et al. 2021.
          • Family Netzeliidae Kosakyan et al. 2016. Genera: Cucurbitella Penard 1902; Cyclopyxis Deflandre 1929; Netzelia Ogden 1979.
    • Order Euamoebida Lepşi 1960 sensu Smirnov et al. 2011^[36]
      • Suborder Amoebina Cavalier-Smith 2016
        • Family Amoebidae Ehrenberg 1838 Page 1987. Genera: Amoeba, Chaos, Polychaos, Parachaos, Trichamoeba, Deuteramoeba, Hydramoeba
        • Family Hartmannellidae Volkonsky 1931. Cashia, Copromyxa, Copromyxella, Glaeseria, Hartmannella, Ptolemeba, Saccamoeba
      • Suborder Nolandina Cavalier-Smith 2016^[36] → family Nolandellidae Cavalier-Smith 2011, Lahr & Katz 2011. Sole genus: Nolandella.

Evosea Kang et al. 2017

• Class Cutosea Cavalier-Smith 2016 → order Squamocutida Cavalier-Smith 2016
  • Family Squamamoebidae Cavalier-Smith 2016. Genera: Armaparvus Schuler & Brown 2019; Squamamoeba Kudryavtsev & Pawlowski 2013.
  • Family Sapocribridae Cavalier-Smith 2016. Sole genus: Sapocribrum Lahr et al. 2015.
  • Family Idionectidae Hess & Simpson 2019. Sole genus: Idionectes Hess & Simpson 2019.^[37]
• Class Variosea^[g] Cavalier-Smith 2004
  • Angulamoeba Berney, Bass & Geisen 2015
  • Arboramoeba Berney, Bass & Geisen 2015
  • Darbyshirella Berney, Bass & Geisen 2015
  • Dictyamoeba Berney, Bass & Geisen 2015
  • Ischnamoeba Berney, Bass & Geisen 2015
  • Heliamoeba Berney, Bass & Geisen 2015
  • Filamoeba Page 1967
  • Phalansterium Cienkowski 1870.
  • Family Flamellidae Lahr & Katz in Lahr et al. 2011.^[38] Genera included: Flamella Schaeffer 1926; Telaepolella Lahr et al. 2012.
  • Order Protosteliida^ICZN/Protosteliales^ICN L.S.Olive & Stoian. 1966 sensu Shadwick & Spiegel in Adl et al. 2012 → family Protosteliidae^ICZN/Protosteliaceae^ICN L.S.Olive & Stoian. 1966. Sole genus: Protostelium L.S.Olive & Stoian. 1960 (includes Planoprotostelium L.S. Olive & Stoian. 1971).
  • Order Fractovitellida Lahr et al. 2011, sensu Kang et al. 2017
    • Family Acramoebidae Smirnov, Nassonova & Cavalier-Smith 2008. Sole genus: Acramoeba Smirnov, Nassonova & Cavalier-Smith 2008.
    • Family Schizoplasmodiidae Shadwick & Spiegel in Adl et al. 2012. Genera: Ceratiomyxella L.S. Olive & Stoian. 1971; Nematostelium L.S. Olive & Stoian. 1970; Schizoplasmodium L.S. Olive & Stoian. 1966.
    • Family Soliformoviidae Lahr & Katz 2011. Genera: Soliformovum Spiegel 1995; Grellamoeba Dyková, Kostka & Pecková 2008.
  • Order Cavosteliida^ICZN/Cavosteliales^ICN Shadwick & Spiegel in Adl et al. 2012 → family Cavosteliidae^ICZN/Cavosteliaceae^ICN Olive & Stoianovitch 1964. Genera: Cavostelium L.S.Olive 1965; Schizoplasmodiopsis L.S.Olive 1967; Tychosporium Spiegel 1995.
  • Order Holomastigida Lauterborn 1895 (includes Artodiscida Cavalier-Smith 2013) → family Multiciliidae Poche 1913 (includes Artodiscidae Cavalier-Smith 2013). Genera: Artodiscus^? Penard 1890; Multicilia Cienkowsky 1881.
• Class Archamoebea Cavalier-Smith 1983, sensu Cavalier-Smith 2004
  • Family Tricholimacidae Cavalier-Smith 2012. Sole genus: Tricholimax Frenzel 1892.
  • Family Entamoebidae Chatton 1925. Sole genus: Entamoeba Casagrandi & Barbagallo 1895.
  • Family Rhizomastixidae Ptáčková et al. 2013. Sole genus: Rhizomastix Aléxéieff 1911.
  • Order Mastigamoebida Frenzel 1897, sensu Cavalier-Smith 2013.^[h] Genera: Endamoeba Leidy 1879; Endolimax Kuenen & Swellengrebel 1917; Iodamoeba Dobell 1919; Mastigamoeba Schulze 1875; Mastigina Frenzel 1897.
  • Order Pelobiontida Page 1976, sensu Cavalier-Smith 2013 → family Pelomyxidae Schulze 1877. Genera: Mastigella Frenzel 1897; Pelomyxa Greef 1874.
• Superclass Eumycetozoa Zopf 1884 sensu Kang et al. 2017 (=Mycetozoa de Bary 1859 ex Rostafinski 1873, Macromycetozoa Fiore-Donno 2010)
  • Class Dictyostelea^ICZN Lister 1909 sensu Sheikh et al. 2018/Dictyosteliomycetes^ICN Doweld 2001. Genus unassigned to an order: Synstelium S.Baldauf S.Sheikh & Thulin 2018. Incertae sedis genus: Coenonia^? Tiegh. 1884.^[39]
    • Order Acytosteliales S.Baldauf S.Sheikh & Thulin 2018
      • Family Acytosteliaceae Raper ex Raper & Quinlan 1958. Genera: Acytostelium Raper 1956; Rostrostelium S.Baldauf, S.Sheikh & Thulin 2018; Heterostelium S.Baldauf, S.Sheikh & Thulin 2018.
      • Family Cavenderiaceae S.Baldauf, S.Sheikh & Thulin 2018. Sole genus: Cavenderia S.Baldauf, S.Sheikh & Thulin 2018.
    • Order Dictyosteliales L.S.Olive ex P.M.Kirk et al. 2001. Genus unassigned to a family: Coremiostelium S.Baldauf S.Sheikh Thulin & Spiegel 2018.
      • Family Dictyosteliaceae Rostaf. ex Cooke 1877. Genera: Dictyostelium Bref. 1869; Polysphondylium Bref. 1884.
      • Family Raperosteliaceae S.Baldauf S.Sheikh & Thulin 2018. Genera: Hagiwaraea S.Baldauf S.Sheikh & Thulin 2018; Raperostelium S.Baldauf S.Sheikh & Thulin 2018; Speleostelium S.Baldauf S.Sheikh & Thulin 2018; Tieghemostelium S.Baldauf S.Sheikh & Thulin 2018.
  • Class Ceratiomyxea^ICZN/Ceratiomyxomycetes^ICN D. Hawksw., B. Sutton & Ainsw. 2019^[4] → order Protosporangiida^ICZN Shadwick & Spiegel in Adl et al. 2012/Ceratiomyxales^ICN G.W. Martin ex M.L. Farr & Alexop.
    • Family Ceratiomyxidae^ICZN/Ceratiomyxaceae^ICN J.Schröt. 1889. Sole genus: Ceratiomyxa J.Schröt. 1889.
    • Family Protosporangiidae^ICZN Spiegel in Adl et al. 2012/Protosporangiaceae^ICN Leontyev, Stephenson, Schnittler, Shchepin & Novozhilov 2020. Genera: Clastostelium L.S. Olive & Stoian. 1972; Protosporangium L.S. Olive & Stoian. 1972.^[40]
  • Class Myxogastrea^ICZN Cavalier-Smith 1993/Myxomycetes^ICN G.Winter 1880 (=Myxogastres Fr. 1829, Myxogasteres Schröt., 1889, Endosporeae Rostaf. 1873, Myxogastromycetidae G.W.Martin 1961, Myxogastromycetes M.Locquin 1974, Myxogastria Cavalier-Smith 2012 as "Myxogastria L.S.Olive 1970" nom. inval.)^[4]
    • Subclass Lucisporinia^ICZN Cavalier-Smith 2013 as "Lucisporidia"/Lucisporomycetidae^ICN Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019.^[4] Incertae sedis genera: Arcyriatella Hochg. & Gottsb. 1989; Calonema Morgan 1893; Minakatella G.Lister 1921; Trichioides Novozh., Hoof & Jagers 2015.
      • Superorder Cribariidia Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019 → order Cribariida^ICZN/Cribariales^ICN T.Macbr. 1922 → family Cribariidae^ICZN/Cribariaceae^ICN Corda 1838. Genera: Cribaria Pers. 1794; Lindbladia Fr. 1849; Licaethalium Rostaf. 1873.^[4]
      • Superorder Trichiidia Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019^[4]
        • Order Reticulariida^ICZN/Reticulariales^ICN Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019 → family Reticulariidae^ICZN/Reticulariaceae^IZN Chevall. ex Corda 1842. Genera: Alwisia Berk. & Broome 1873 emend. Leontyev, Schnittler, G.Moreno, S.L.Stephenson, D.W.Mitchell & C.Rojas 2014; Lycogala Adans. 1763; Reticularia Bull. 1787–1788; Tubifera J.F.Gmel. 1792 emend. Lentyev, Schnittler & S.L.Stephenson 2015.^[4]
        • Order Liceida^ICZN/Liceales^ICN E. Jahn 1928 → family Liceidae^ICZN/Liceaceae^ICN Chevall. 1826. Genera: Licea Schrad. 1797; Listerella^? E.Jahn 1907.^[4]
        • Order Trichiida^ICZN/Trichiales^ICN T.Macbr. 1922^[4]
          • Family Dianematidae^ICZN/Dianemataceae^ICN T.Macbr. 1922. Genera: Calomyxa Nieuwl. 1916; Dianema Rex. 1891; Dictydiaethalium Rostaf. 1873; Prototrichia Rostaf. 1876.
          • Family Trichiidae^ICZN/Trichiaceae^ICN Chevall. 1826 sensu Martin & Alexopoulos 1969. Genera: Hemitrichia Rostaf. 1873 (includes Trichia decipiens); Arcyria F.H.Wigg. 1780 (includes Arcyodes O.F.Cook 1902); Perichaena^(P) Fr. 1817; Trichia Haller 1768 (includes Cornuvia Rostaf. 1873, Metatrichia Ing 1964, Oligonema Rostaf. 1875).
    • Subclass Columellinia^ICZN Cavalier-Smith 2013 as "Columellidia"/Columellomycetidae^ICN Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019 (=Fuscisporidia Cavalier-Smith 2013 sensu Kretzschmar et al. 2015). Incertae sedis genera: Diachea Fr. 1825; Echinosteliopsis Reinhardt & L.S.Olive 1967; Leptoderma G.Lister 1913; Paradiachea Hertel 1956; Protophysarum M.Blackw. & Alexop. 1975; Trabrooksia H.W.Keller 1980; Willkommlangea Kuntze 1891.^[4]
      • Superorder Echinosteliidia Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019 → order Echinosteliida^ICZN/Echinosteliales^ICN G. W. Martin 1961 → family Echinosteliidae^ICZN/Echinosteliaceae Rostaf. ex Cooke 1877. Genera: Barbeyella Meyl. 1914; Echinostelium de Bary in Rostafiński 1873 (includes Semimorula E.F.Haskins, McGuinn & C.S.Berry 1983).^[4]
      • Superorder Stemonitidia Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019 (=Fuscisporidia Cavalier-Smith 2013 non sensu Kretzschmar et al. 2016)^[4]
        • Order Clastodermatida^ICZN/Clastodermatales^ICN Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019 → family Clastodermatidae^ICZN/Clastodermataceae^ICN Alexop. & T.E. Brooks 1971. Sole genus: Clastoderma A.Blytt 1880.
        • Order Meridermatida^ICZN/Meridermatales^ICN Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019 → family Meridermatidae^ICZN/Meridermataceae^ICN Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019. Sole genus: Meriderma Mar.Mey. & Poulain in Poulain, Meyer & Bozonnet 2011.
        • Order Stemonitida^ICZN/Stemonitidales^ICN T.Macbr. 1922 as "Stemonitales" emend. Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019
          • Family Stemonitidae^ICZN/Stemonitidaceae^ICN Fr. 1829 emend. Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019. Genera: Macbrideola H.C.Gilbert 1934; Stemonitis Gled. 1753; Symphytocarpus Ing & Nann.-Bremek. 1967.
          • Family Amaurochaetidae^ICZN/Amaurochaetaceae ^ICN Rostaf. ex Cooke 1877 emend. Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019. Genera: Comatricha Preuss 1851; Stemonaria Nann.-Bremek., R.Sharma & Y.Yamam. in Nannenga-Bremekamp, Yamamoto & Sharma 1984; Stemonitopsis (Nann.-Bremek.) Nann.-Bremek. 1975; Amaurochaete Rostaf. 1873; Brefeldia Rostaf. 1873; Enerthenema Bowman 1830; Paradiacheopsis Hertel. 1954.
        • Order Physarida^ICZN/Physarales^ICN T.Macbr. 1922. Genus not assigned to a family: Tasmaniomyxa Lloyd et al. 2023.^[41]
          • Family Lamprodermatidae^ICZN/Lamprodermataceae^ICN T.Macbr. 1899 emend. Leontyev, Schnittler, S.L.Stephenson, Novozhilov & Shchepin 2019. Genera: Lamproderma Rostaf. (includes Dichaeopsis Meyl. 1930, Colloderma G.Lister 1910, Elaeomyxa Hagelst. 1942); Collaria^(P) Nann.-Bremek. 1967.
          • Family Didymiidae^ICZN/Didymiaceae^ICN Rostaf. ex Cooke 1877. Genera: Diderma Pers. 1794; Didymium Schrad. 1797; Lepidoderma de Bary in Rostafiński 1873; Mucilago Battarra 1755.
          • Family Physaridae^ICZN/Physaraceae^ICN Chevall. 1826. Genera: Craterium Trentep. in Roth 1797; Leocarpus Link 1809; Fuligo Haller 1768; Physarum Pers. 1794 (includes Badhamia Berk. 1852); Physarella Peck. 1882; Physarina Höhn. 1909; Kelleromyxa Eliasson in Eliasson, Keller & Schoknecht 1991.

Class Discosea Cavalier-Smith et al. 2004 sensu Smirnov et al. 2011

• Subclass Flabellinia Smirnov et al. 2005. Incertae sedis genera: Microglomus Olive & Stoianovitch 1977; Mycamoeba Blandenier, Seppey, Singer, Vlimant, Simon, Duckert & Lara 2016.^[i][43]
  • Order Stygamoebida^(P) Smirnov & Cavalier-Smith in Smirnov et al. 2011 → family Stygamoebidae Smirnov & Cavalier-Smith in Smirnov et al. 2011. Genera: Stygamoeba Sawyer 1975; Vermistella Moran, Anderson, Dennett, Caron & Gast 2007.^[j]
  • Order Dermamoebida Cavalier-Smith 2004 emend. Kudryavtsev, Voytinsky & Volkova 2022^[44]
    • Family Dermamoebidae Cavalier-Smith & Smirnov 2011. Genera: Dermamoeba Page & Blakey 1979; Paradermamoeba Smirnov & Goodkov 1993; Coronamoeba Kudryavtsev, Voytinsky & Volkova 2022.^[44]
    • Family Mayorellidae Schaeffer 1926. Sole genus: Mayorella Schaeffer 1926.
  • Order Thecamoebida^[h] Schaeffer 1926, sensu Smirnov & Cavalier-Smith 2011. Genera: Sappinia Dangeard 1896; Stenamoeba Smirnov et al. 2007; Stratorugosa Melton & Tekle 2019;^[45] Thecamoeba Fromentel 1874; Thecochaos Page 1981.^[46]
  • Order Dactylopodida^[h] Smirnov et al. 2005 sensu Kang et al. 2017. Genera: Cunea Kudryavtsev & Pawlowski 2015; Janickina^? Chatton 1953; Korotnevella Goodkov 1988; Neoparamoeba Page 1987; Paramoeba Schaudinn 1896; Pseudoparamoeba Page 1979; Vexillifera Schaeffer 1926.
  • Order Vannellida Smirnov et al. 2005 → family Vannellidae Bovee 1979. Genera: Clydonella Sawyer 1975; Lingulamoeba Sawyer 1975; Paravannella Kudryavtsev 2014; Pessonella^? Pussard 1973;^[k] Ripella Smirnov et al. 2007; Vannella Bovee 1965.
• Subclass Centramoebia Cavalier-Smith et al. 2016^[36]
  • Order Acanthopodida^[h] Page 1976 (=Centramoebida Rogerson & Patterson 2002, sensu Tice et al. 2016).^[47] Genera: Acanthamoeba Volkonsky 1931; Balamuthia Visvesvara et al. 1993; Luapeleamoeba Shadwick & Spiegel 2016; Protacanthamoeba Page 1981; Dracoamoeba Tice & Brown 2016; Vacuolamoeba Tice, Geisen & Brown 2016.
  • Order Himatismenida^[h] Page 1987. Genera: Cochliopodium Hertwig & Lesser 1874; Ovalopodium Sawyer 1980; Parvamoeba Rogerson 1993.
  • Order Pellitida^[h] Smirnov & Cavalier-Smith 2011, sensu Kang et al. 2017. Genera: Endostelium L.S.Olive, Bennett & Deasey 1984; Gocevia Valkanov 1932; Paragocevia^? Page 1987; Pellita Smirnov & Kudryavtsev 2005.

Diaphoretickes Adl et al. 2012

• Order Microhelida Cavalier-Smith & Chao in Yabuki et al. 2012 → family Microheliellidae Cavalier-Smith & Chao in Yabuki et al. 2012. Sole genus: Microheliella Cavalier-Smith & Chao in Yabuki et al. 2012.^[l]
• Phylum Telonemia^[m] Shalchian-Tabrizi 2006 → class Telonemea Cavalier-Smith 1993 → order Telonemida Cavalier-Smith 1993 → family Telonemidae Cavalier-Smith 1993. Genera: Arpakorses Tikhonenkov & Karpov 2022;^[48] Lateronema Cavalier-Smith 2015; Telonema Griessmann 1913.

Archaeplastida Adl et al. 2005

• Division Glaucophyta Skuja 1954 (=Glaucocystaceae West 1904, Glaucocystophyta Kies and Kremer 1986, Glaucoplantae Marin & Melkonian in Li et al. 2020). Incertae sedis genera: Archaeopsis, Chalarodora, Glaucocystopsis, Peliaina, Strobilomonas.^[5]
  • Order Cyanophorales Kies & Kremer 2006. Sole genus: Cyanophora.
  • Order Glaucocystales Bessey 1907. Sole genus: Glaucocystis.
  • Order Gloeochaetales Bessey 1907. Genera: Cyanoptyche, Gloeochaete.
• Phylum Picozoa Seenivasan, Sausen, Medlin & Melkonian 2013 (=picobiliphytes Not et al. 2007) → class Picomonadea Seenivasan, Sausen, Medlin & Melkonian 2013 → order Picomonadida Seenivasan, Sausen, Medlin & Melkonian 2013 → family Picomonadidae Seenivasan, Sausen, Medlin & Melkonian 2013. Sole genus: Picomonas Seenivasan, Sausen, Medlin & Melkonian 2013.^[n]
• Phylum Rhodelphidia Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019 → class Rhodelphidea Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019 → order Rhodelphida Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019 → family Rhodelphidae Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019. Sole genus: Rhodelphis Tikhonenkov, Gawryluk, Mylnikov & Keeling 2019.^[50]
• Division Rhodophyta Wettstein 1901 (=Rhodophyceae Thuret 1855, emend. Rabenhorst 1863, Rhodoplantae Saunders and Hommersand 2004 emend. Adl et al. 2005)

Chloroplastida Adl et al. 2006

• Division Prasinodermophyta Marin & Melkonian in Li et al. 2020^[51]
  • Class Prasinodermophyceae Marin & Melkonian in Li et al. 2020 → order Prasinodermatales Marin & Melkonian in Li et al. 2020 → family Prasinodermataceae Marin & Melkonian in Li et al. 2020. Sole genus: Prasinoderma Hasegawa & Chihara in Hasegawa et al. 1996.
  • Class Palmophyllophyceae Leliaert et al. 2016 emend. Marin & Melkonian in Li et al. 2020
    • Order Palmophyllales Zechman, Verbruggen, Leliaert, Ashwort, M.A.Buchheim, Fawley, H.Spalding, Pueschel, J.A.Buschheim, Verghese & Hanisak 2010 → family Palmophyllaceae Zechman, Verbruggen, Leliaert, Ashwort, M.A.Buchheim, Fawley, H.Spalding, Pueschel, J.A.Buschheim, Verghese & Hanisak 2010. Genera: Palmophyllum Kützing 1849; Verdigellas Ballantine & Norris 1994; Palmoclathrus^? Womersley 1971.^[52]
    • Order Prasinococcales Guillou et al. ex Leliaert et al. 2016 emend. Marin & Melkonian in Li et al. 2020 → family Prasinococcaceae Leliaert et al. 2016. Sole genus: Prasinococcus Miyashita & Chihara in Miyashita et al. 1993.
• Division Chlorophyta Reichenbach 1828 emend. Pascher 1914 emend. Lewis & McCourt 2004
  • Class Chloropicophyceae Lopes dos Santos & Eikrem 2017 → order Chloropicales Lopes dos Santos & Eikrem 2017 → family Chloropicaceae Lopes dos Santos & Eikrem 2017. Genera: Chloroparvula Lopes dos Santos & Eikrem 2017; Chloropicon Lopes dos Santos & Eikrem 2017.
  • Class Mamiellophyceae Marin & Melkonian 2010
    • Order Mamiellales Moestrup 1984 emend. Marin & Melkonian 2010
      • Family Bathycoccaceae Marin & Melkonian 2010. Genera: Bathycoccus Eikrem & Throndsen 1990; Ostreococcus Courties & Chrétiennot-Dinet 1995.
      • Family Mamiellaceae Moestrup 1984 emend. Marin & Melkonian 2010. Genera: Mamiella Moestrup 1984; Mantoniella Desikachary 1972; Micromonas Manton & Parke 1960.
    • Order Dolichomastigales Marin & Melkonian 2010
      • Family Crustomastigaceae Marin & Melkonian 2010. Sole genus: Crustomastix Nakayama, Kawachi & Inouye 2000.
      • Family Dolichomastigaceae Marin & Melkonian 2010. Sole genus: Dolichomastix Manton 1977.
    • Order Monomastigales R.E.Norris ex Marin & Melkonian 2010 (=Monomastigales Norris in Parker 1982 nomen nudum) → family Monomastigaceae Marin & Melkonian 2010. Sole genus: Monomastix Scherffel 1912.
  • Class Nephroselmidophyceae Cavalier-Smith 1993 emend. Yamaguchi 2011 → order Nephroselmidales Nakayama, Suda, Kawachi & Inouye 2007 → family Nephroselmidaceae Pascher 1913 ex Silva 1980. Genera: Nephroselmis Stein 1878.
  • Class Picocystophyceae Lopes dos Santos & Eikrem 2017 → order Picocystales Lopes dos Santos & Eikrem 2017 → family Picocystaceae Lopes dos Santos & Eikrem 2017. Sole genus: Picocystis R.A.Lewin in Lewin et al. 2000.
  • Class Pseudoscourfieldiophyceae Crépeault, C.Otis, Pombert, Turmel & Lemieu 2024 → order Pseudoscourfieldiales Melkonian 1990 ex Crépeault, C.Otis, Pombert, Turmel & Lemieu 2024 → family Pseudoscourfieldiaceae Melkonian 1990 ex Crépeault, C.Otis, Pombert, Turmel & Lemieu 2024 (=Pycnococcaceae Guillard in Guillard, Keller, O'Kelly & Floyd 1991 emend. M.W.Fawley in Fawley et al. 1999. Sole genus: Pseudoscourfieldia Manton 1975 (=Pycnococcus Guillard in Guillard, Keller, O'Kelly & Floyd 1991).^[53]
  • Class Pyramimonadophyceae Moestrup & Daugbjerg in Daugbjerg et al. 2020^[54] → order Pyramimonadales Chadefaud 1950
    • Family Pyramimonadaceae Korshikov 1938. Genera: Cymbomonas Schiller 1913; Pyramimonas Schmarda 1850; "Prasinopapilla" (not formally described).
    • Family Halosphaeraceae Haeckel 1894. Genera: Halosphaera Schmitz 1878; Pachysphaera Ostenfeld 1899; †Tasmanites^? E.Newton 1875.
  • Core Chlorophyta
    • Class Chlorodendrophyceae Massjuk 2006 → order Chlorodendrales Berger 1954 as "Chlorodendrinales" (=Tetraselmidales Ettl. 1982) → family Chlorodendraceae Oltmanns 1904. Genera: Prasinocladus Kuckuck 1894; Scherffelia Pascher 1912; Tetraselmis Stein 1878.
    • Class Pedinophyceae Moestrup 1991 emend. Fawley, Zechman & Buchheim in Adl et al. 2012^[55]
      • Order Marsupiomonadales Marin 2012
        • Family Marsupiomonadaceae Marin 2012. Sole genus: Marsupiomonas Jones, Leadbeater & Green 1994.
        • Family Resultomonadaceae Marin 2012. Sole genus: Resultomonas Marin 2012.
      • Order Pedinomonadales Moestrup 1991 emend. Marin 2012 → family Pedinomonadaceae Korshikov 1938. Genera: Chlorochytridion Vischer 1945; Pedinomonas Korshikov 1923.
    • UTC clade
      • Class Chlorophyceae Wille 1884
        • SV clade^[56]
          • Order Sphaeropleales^(P?) Luerssen 1877. Incertae sedis genera: Spermatozopsis Korshikov 1913; Golenkinia Chodat 1894; Jenufa Němcová, M.Eliáš, Škaloud & Neustupa 2011; Johansenicoccus.^[57][56][58]
            • Family Dictyochloridaceae Fučíková, P.O.Lewis & L.A.Lewis 2013. Sole genus: Dictyochloris Vischer 1945.
            • Family Sphaeropleaceae Kützing 1849
            • Family Microsporaceae Bohlin 1901
            • Treubarinia. Genera: Trochiscia Kützing 1834; Treubaria C.Bernard 1908; Cylindrocapsa Reinsch 1867; Elakatothrix Wille 1898.^[56]
            • Scenedesminia ("traditional" Sphaeropleales)^[56]
              • Family Bracteacoccaceae P.M.Tsarenko 2005. Sole genus: Bracteacoccus Tereg 1922.
              • Family Bracteamorphaceae Fučíková, P.O.Lewis & L.A.Lewis 2013. Sole genus: Bracteamorpha Fučíková, P.O.Lewis & L.A.Lewis 2013.
              • Family Chromochloridaceae Fučíková, P.O.Lewis & L.A.Lewis 2013. Sole genus: Chromochloris Kol & Chodat 1934.
              • Family Dictyococcaceae^? Fučíková, P.O.Lewis & L.A.Lewis 2013. Sole genus: Dictyococcus Gerneck 1907.
              • Family Hydrodictyaceae Dumortier 1829. Genera: Hydrodictyon Roth; Lacunastrum H.A.McManus; Monactinus Corda; Parapediastrum^(P) E.Hegewald; Pediastrum Meyen.^[59]
              • Family Mychonastaceae Fučíková, P.O.Lewis & L.A.Lewis 2013. Sole genus: Mychonastes P.D.Simpson & S.D.Van Valkenburg 1978.
              • Family Neochloridaceae Ettl & Komárek 1982
              • Family Pseudomuriellaceae Fučíková, P.O.Lewis & L.A.Lewis 2013. Sole genus: Pseudomuriella N.Hanagata 1998.
              • Family Scenedesmaceae Oltmanns 1904
              • Family Schizochlamydaceae Fučíková, P.O.Lewis & L.A.Lewis 2013. Sole genus: Schizochlamys Braun ex Kützing 1849.
              • Family Selenastraceae Blackman & Tansley 1903 (=Ankistrodesmaceae Korshikov 1953)
              • Family Radiococcaceae
              • Family Rotundellaceae Fučíková, P.O.Lewis & L.A.Lewis 2013. Sole genus: Rotundella Fučíková, P.O.Lewis & L.A.Lewis 2013.
              • Family Tumidellaceae Fučíková, P.O.Lewis & L.A.Lewis 2013. Sole genus: Tumidella Fučíková, P.O.Lewis & L.A.Lewis 2013.
          • Order Volvocales Poche 1913
        • OCC clade^[56][58]
          • Order Chaetopeltidales O'Kelly, Watanabe & Floyd
          • Order Chaetophorales Wille 1901
          • Order Oedogoniales Heering 1914
      • Class Trebouxiophyceae Friedl 1995 (=Pleurastrophyceae Mattox et al. 1984)
      • Class Ulvophyceae^(P)
• Division Streptophyta Bremer & Wanntorp 1981 (=Charophyta Migula 1897 emend. Karol et al. 2009)
  • Class Chlorokybophyceae Irisarri et al. 2021 → order Chlorokybales Irisarri et al. 2021 → family Chlorokybaceae Irisarri et al. 2021. Sole genus: Chlorokybus Geitler 1942.^[60]
  • Class Mesostigmatophyceae Marin & Melkonian 1999 emend. Lewis & McCourt 2004 (=Mesostigmata Turmel et al. 2002) → order Mesostigmales Cavalier-Smith 1998 → family Mesostigmataceae Fott 1947. Sole genus: Mesostigma Lauterborn 1894.
  • Class Klebsormidiophyceae C. Jeffrey ex Guiry 2023^[61]
    • Order Klebsormidiales Bierenbroodspot et al. 2024 → family Klebsormidiaceae Bierenbroodspot et al. 2024. Genera: Klebsormidium Silva, Mattox & Blackwell 1972; Interfilum Chodat 1992; Streptofilum Mikhailyuk & Lukešová 2018.
    • Order Entransiales Bierenbroodspot et al. 2024 → family Entransiaceae Bierenbroodspot et al. 2024. Sole genus: Entransia E.O. Hughes 1948.
    • Order Hormidiellales Bierenbroodspot et al. 2024 → family Hormidiellaceae Bierenbroodspot et al. 2024. Genera: Hormidiella Iyengar & Kanthamma 1940; Streptosarcina Mikhailyuk & Lukešová 2018.
  • Phragmoplastophyta Lecointre & Guyander 2006
    • Class Charophyceae Smith 1938 emend. Karol et al. 2009
    • Class Coleochaetophyceae Jeffrey 1982
    • Anydrophyta Rensing 2020^[62]
      • Class Zygnematophyceae van den Hoek et al. 1995 emend. Hall et al. 2009^[63]
        • Order Serritaeniales S.Hess & J.de Vries 2022 → family Serritaeniaceae S.Hess & J.de Vries 2022. Sole genus: Serritaenia A.Busch & S.Hess 2021.
        • Order Zygnematales Bessey 1907 emend. Hess & de Vries 2022 → family Zygnemataceae Kützing 1843. Genera: Cylindrocystis Meneghini 1848; Mesotaenium^? Nägeli 1849; Mougeotia (Roth) C.Agardh 1824; Zygnema C.Agardh 1817 nom. cons.; Zygnemopsis (Skuja) Transeau 1934.
        • Order Desmidiales Bessey 1907 emend. S.Hess & J.de Vries 2022 → family Desmidiaceae Ralfs 1848. Genera: Bambusina Kützing ex Kützing 1849 nom. cons.; Closterium Nitzsch ex Ralfs 1848; Cosmarium Corda ex Ralfs 1848; Cosmocladium Brébisson 1856; Desmidium C.Agardh ex Ralfs 1848; Euastrum Ehrenberg ex Ralfs 1848; Micrasterias C.Agardh ex Ralfs 1848; Netrium (Nägeli) Itzigsohn & Rothe 1856; Nucleotaenium Gontcharov & Melkonian 2010; Onychonema G.C.Wallich 1860; Penium Brébisson ex Ralfs 1848; Phymatodocis Nordstedt 1878; Planotaenium (Ohtani) Petlovany & Palamar-Mordvintseva 2009; Pleurotaenium Nägeli 1849; Staurastrum Meyen ex Ralfs 1848; Staurodesmus Teiling 1948; Xanthidium Ehrenberg ex Ralfs 1848; etc.
        • Order Spirogyrales Clements nom. cons. emend. Hess & de Vries 2022. Sole genus: Spirogyra Link 1820 nom. cons.
      • Kingdom Embryophyta Engler 1886 emend. Lewis & McCourt 2004 (=Plantae Haeckel 1866). Excluded from protists.

Stramenopiles Patterson 1989, emend. Adl et al. 2005

• Class Platysulcea Cavalier-Smith 2018 → order Platysulcida Cavalier-Smith 2018 → family Platysulcidae Shiratori, Nakayama & Ishida 2015. Sole genus: Platysulcus Shiratori, Nakayama & Ishida 2015.
• Family Kaonashiidae Weston, Eglit & Simpson 2023. Sole genus: Kaonashia Weston, Eglit & Simpson 2023.^[64]

Phylum Bigyra Cavalier-Smith 1998 emend. 2006

• Subphylum Opalozoa Cavalier Smith 1991 emend. 2006
  • Infraphylum Placidozoa Cavalier-Smith 2013
    • Class Placididea Moriya, Nakayama & Inouye 2002 → order Placidida Moriya, Nakayama & Inouye 2002 → family Placididae Moriya, Nakayama & Inouye 2002. Genera: Allegra Rybarski & Arndt 2021; Haloplacidia Rybarski, Nitsche & Arndt 2021; Pendulomonas S.M.Tong 1997; Placidia Moriya, Nakayama & Inouye 2002; Placilonga Rybarski & Arndt 2021; Suigetsumonas Okamura & Kondo 2015; Wobblia Moriya, Nakayama & Inouye 2000.^[65]
    • Class Nanomonadea Cavalier-Smith in Cavalier-Smith & Scoble 2013 (=clade MAST-3) → order Uniciliatida Cavalier-Smith in Cavalier-Smith & Scoble 2013
      • Family Incisomonadidae Cavalier-Smith in Cavalier-Smith & Scoble 2013. Sole genus: Incisomonas Scoble & Cavalier-Smith 2013.
      • Family Solenicolidae Cavalier-Smith in Cavalier-Smith & Scoble 2013. Sole genus: Solenicola Pavillard 1916.
    • Class Opalomonadea Cavalier-Smith 2013 (=clade MAST-12). No described species.
    • Superclass Opalinata Wenyon 1926 emend. Cavalier-Smith 1997
      • Class Opalinea Wenyon 1926 (=Slopalinida Patterson 1985)^[66]
        • Order Proteromonadida Grassé 1952 emend. Cavalier-Smith 1993 → family Proteromonadidae Grassé 1952. Sole genus: Proteromonas Kunstler 1883 (= Prowazekella Aléxéieff 1912).
        • Order Opalinida Poche 1913 stat. nov. Hall 1953 emend. Cavalier-Smith
          • Family Karotomorphidae Travis 1934. Sole genus: Karotomorpha Travis 1934.
          • Family Opalinidae Claus 1874. Genera: Cepedea Metcalf 1920; Opalina Purkinje & Valentin 1835; Protoopalina Metcalf 1918; Protozelleriella Delvinquier et al. 1991; Zelleriella Metcalf 1920.
      • Class Blastocystea Zierdt et al. 1967 → order Blastocystida Zierdt 1978 → family Blastocystidae Jiang & He 1988. Sole genus: Blastocystis Alexeieff 1911.
  • Infraphylum Bikosea Cavalier-Smith 2018 (=Bicosoecida Grassé 1926 emend. Karpov 1998) → class Bikosea Cavalier-Smith 1986 as "Bicosoecea" orth. em. 2013. Genera not assigned to families: Bilabrum Schoenle & Arndt in Schoenle et al. 2020;^[67] Cafileria Jirsová, Füssy, Richtová, Gruber, & Oborník 2019;^[68] Cantina Yubuki et al. 2015.
    • Family Pseudobodonidae^? Cavalier-Smith in Cavalier-Smith & Scoble 2013. Sole genus: Pseudobodo Griessmann 1913.^[69]
    • Subclass Rictidia Cavalier-Smith in Cavalier-Smith & Scoble 2013 → order Rictida Cavalier-Smith in Cavalier-Smith & Scoble 2013 → family Rictidae Cavalier-Smith in Cavalier-Smith & Scoble 2013. Sole genus: Rictus Yubuki, Leander & Silberman 2010.
    • Subclass Bicosidia^ICZN/Bicosoecophycidae^ICN Cavalier-Smith in Cavalier-Smith & Chao 2006
      • Superorder Borokiae Cavalier-Smith in Cavalier-Smith & Chao 2006 → order Borokida^ICZN/Borokales^ICN Cavalier-Smith in Cavalier-Smith & Chao 2006 → family Borokidae^ICZN/Borokaceae^ICN Cavalier-Smith in Cavalier-Smith & Chao 2006. Sole genus: Boroka Cavalier-Smith in Cavalier-Smith & Chao 2006.
      • Superorder Cyathobodoniae Cavalier-Smith 1993 emend. 2006. Incertae sedis genus: Halocafeteria Park, Cho & Simpson 2006.^[67]
        • Order Anoecida^ICZN/Anoecales^ICN Cavalier-Smith 1997^[o]
          • Family Anoecidae^ICZN/Anoecaceae^ICN Cavalier-Smith in Cavalier-Smith & Chao 2006. Sole genus: Anoeca Cavalier-Smith in Cavalier-Smith & Chao 2006.
          • Family Caecitellidae^ICZN/Caecitellaceae^ICN Cavalier-Smith in Cavalier-Smith & Chao 2006. Sole genus: Caecitellus Patterson et al. 1993.
          • Family Cafeteriidae^ICZN/Cafeteriaceae^ICN Moestrup 1995. Sole genus: Cafeteria Fenchel & Patterson 1988.
          • Family Symbiomonadaceae Cavalier-Smith in Cavalier-Smith & Chao 2006. Sole genus: Symbiomonas Guillou & Chretiennot-Dinet 1999.
        • Order Bicoecida^ICZN/Bicoecales^ICN Grassé 1926
          • Family Bicosoecidae Stein 1878. Genera: Bicosoeca James-Clark 1866; Stephanocodon Pascher 1942; Poteriodendron.
          • Family Labromonadidae Cavalier-Smith in Cavalier-Smith & Chao 2006. Sole genus: Labromonas Cavalier-Smith in Cavalier-Smith & Chao 2006.
        • Order Pseudodendromonadida^ICZN/Pseudodendromonadales^ICN Hibberd 1985 emend. Cavalier-Smith 2006.
          • Family Pseudodendromonadidae^ICZN/Pseudodendromonadaceae^ICN Karpov 2000. Genera: Cyathobodo Petersen & Hansen 1961; Pseudodendromonas Bourrelly 1953.
          • Family Siluaniidae^ICZN/Siluaniaceae^ICN Karpov 1998. Genera: Adriamonas Verhagen, Zölffel, Brugerolle & D.J.Patterson 1994; Siluania Karpov 1998; Otto Harder, Ekelund & Karpov 2014; Regin Harder, Ekelund & Karpov 2014.^[70]
          • Family Paramonadidae^ICZN/Paramonadaceae^ICN Kent 1880. Sole genus: Paramonas Kent 1881.
          • Family Nanidae^ICZN/Nanaceae^ICN Cavalier-Smith in Cavalier-Smith & Scoble 2013. Sole genus: Nanum Kim et al. 2010 as "Nanos".
          • Family Neradidae^ICZN/Neradaceae^ICN Cavalier-Smith in Cavalier-Smith & Chao 2006. Sole genus: Nerada Cavalier-Smith in Cavalier-Smith & Chao 2006.
          • Family Filidae^ICZN/Filaceae^ICN Cavalier-Smith in Cavalier-Smith & Scoble 2013. Sole genus: Filos Kim et al. 2010.
• Subphylum Sagenista Cavalier-Smith 1995
  • Class Labyrinthulomycetes Arx 1970 ex Dick 2001 (=Labyrinthulea L.S.Olive 1975 ex Cavalier-Smith 1989, 'phylum' Labyrinthomorpha^ICZN Page in Levine et al. 1980/Labyrinthulomycota^ICN Whittaker 1969)^[71]
    • Order Amphitremida (Poche 1913) Gomaa et al. 2013
      • Family Amphitremidae Poche 1913. Genera: Amphitrema; Archerella; Paramphitrema.
      • Family Diplophryidae Cavalier-Smith in Anderson & Cavalier-Smith 2012. Sole genus: Diplophrys Barker 1868.
    • Order Amphifilida Cavalier-Smith in Anderson & Cavalier-Smith 2012 as "Amphifiloidea"
      • Family Amphifilidae Cavalier-Smith in Anderson & Cavalier-Smith 2012. Sole genus: Amphifila Cavalier-Smith in Anderson & Cavalier-Smith 2012.
      • Family Sorodiplophryidae Cavalier-Smith in Anderson & Cavalier-Smith 2012. Genera: Fibrophrys Takahashi, Yoshida, Inouye & Watanabe 2016; Sorodiplophrys Cienkowski 1876.
    • Order Oblongichytrida^ICZN/Oblongichytriales^ICN Bennett et al. 2017 → family Oblongichytriidae^ICZN/Oblongichytriaceae^ICN Cavalier-Smith in Anderson & Cavalier-Smith 2012. Sole genus: Oblongichytrium R.Yokoyama & D.Honda 2006.
    • Order Labyrinthulida^ICZN Doffein 1901/Labyrinthulales^ICN E.A.Bessey 1950
      • Family Aplanochytriidae^ICZN/Aplanochytriaceae^ICN Leander ex Cavalier-Smith in Anderson & Cavalier-Smith 2012. Sole genus: Aplanochytrium Bahnweg & Sparrow 1972 emend. C.A.Leander & D.Porter 2000 (=Labyrinthuloides F.O.Perkins 1973).
      • Family Labyrinthulidae^ICZN Cienkowski 1867/Labyrinthulaceae^ICN Haeckel 1868. Sole genus: Labyrinthula Cienkowski 1864 (=Chlamydomyxa Archer 1875, Pseudoplasmodium Molisch 1926, Labyrinthodictyon Valkanov 1969, Labyrinthorhiza Chadefaud 1956).
      • Family-level clade "Stellarchytriidae^ICZN/Stellarchytriaceae^ICN". Sole genus: Stellarchytrium FioRito & Leander 2016.
    • Order Thraustochytrida^ICZN/Thraustochytriales^ICN Sparrow 1943
      • Family Althorniidae^ICZN/Althornidiaceae^ICN Jones & Alderman 1973. Sole genus: Althornia Jones & Alderman 1971.
      • Family Thraustochytriidae^ICZN/Thraustochytriaceae^ICN Sparrow ex Cejp 1959. Genera: Aurantiochytrium R.Yokoyama & D.Honda 2006; Botryochytrium R.Yokoyama, B.Salleh & D.Honda 2007; Japonochytrium Kobayasi & M.Ookubo 1953; Monorhizochytrium K.Doi & D.Honda 2017; Parietichytrium R.Yokoyama, B.Salleh & D.Honda 2007; Phycophthorum Hassett 2020;^[72] Schizochytrium S.Goldst. & Belsky 1964 emend. R.Yokoyama & D.Honda 2006; Sicyoidochytrium R.Yokoyama, B.Salleh & D.Honda 2007; Thraustochytrium Sparrow 1936 emend. T.W.Johnson in Johnson & Sparrow 1961; Ulkenia A.Gaertn. 1977 emend. R.Yokoyama, B.Salleh & D.Honda 2007.
  • Class Eogyrea Cavalier-Smith 2013 (=clade MAST-6). Genera not assigned to families: Mastreximonas Lax, Cho & Keeling 2024; Vomastromonas Tikhonenkov, Prokina, Cho & Keeling 2024.^[73]
    • Order Eogyrida Cavalier-Smith 2018^[74] → family Pseudophyllomitidae^ICZN/Pseudophyllomitaceae^ICN Shiratori et al. 2017.^[75] Sole genus: Pseudophyllomitus Lee 2002.

Phylum Gyrista Cavalier-Smith 1998

• Subphylum Bigyromonada Cavalier-Smith 1998^[76]
  • Class Developea Karpov & Aleoshin 2016 ex Cavalier-Smith 2017 → order Developayellida^ICZN Cavalier-Smith 1987 ex 2017/Developayellales^ICN Doweld 2001 → family Developayellidae^ICZN/Developayellaceae^ICN Cavalier-Smith 1997 ex 2017. Genera: Cubaremonas Tikhonenkov, Cho & Keeling 2022; Develocanicus Tikhonenkov, Cho, Mylnikov & Keeling 2022; Develocauda Tikhonenkov, Cho & Keeling 2022; Developayella Tong 1995; Develorapax Karpov & Aleoshin 2016; Mediocremonas del Campo & Weiler 2020.
  • Class Pirsonea Cavalier-Smith 2017 → order Pirsoniales Cavalier-Smith 1998 emend. Prokina et al. 2024 → Pirsoniaceae Cavalier-Smith 1998 emend. Prokina et al. 2024. Genera: Bordeauxia Prokina et al. 2024; Bullionia Prokina et al. 2024; Feodosia Prokina et al. 2024; Koktebelia Prokina et al. 2024; Noirmoutieria Prokina et al. 2024; Pirsonia Schnepf, Debres & Elbrachter 1990.^[77]
• Subphylum Pseudofungi Cavalier-Smith 1986 (=Heterokontimycotina M.W. Dick 1976, Peronosporomycotina M.W.Dick 2001)^[78]: 288
  • Class Hyphochytrea^ICZN Cavalier-Smith 1986/Hyphochytriomycetes^ICN Sparrow ex M.W.Dick 1983 → order Hyphochytriales Sparrow 1960
    • Family Anisolpidiaceae Karling 1943 emend. Dick 2001. Genera: Anisolpidium Karling 1943; Canteriomyces Sparrow 1960.
    • Family Hyphochytridiomycetaceae Fischer 1892 emend. Karling 1939. Sole genus: Hyphochytrium Karling 1939.
    • Family Rhizidiomycetaceae Karling 1943. Latrostium Zopf 1894; Rhizidiomyces Zopf 1884; Rhizidiomycopsis Sparrow 1960.
  • Class Oomycetes Winter 1897, emend. Dick 1976 (=Peronosporomycetes Dick 2001). Incertae sedis genera: Atkinsiella Vishniac 1958; Ciliatomyces Foissner & Foissner 1995 (=Ciliomyces Foissner & Foissner 1986);^[79] Crypticola Humber et al. 1989; Ectrogella Zopf 1884; Eurychasma Magnus 1905; Halodaphnea M.W.Dick 1998; Haliphthoros Vishniac 1958; Haptoglossa Drechsler 1940; Lagena Vanterp. & Ledingham 1930; Lagenisma Drebes 1968; Olpidiopsis Cornu 1872; Pontisma H.E. Petersen 1905; Pythiella Couch 1935; Rozellopsis Karling 1942; Sirolpidium H.E.Petersen 1905.
    • Saprolegnialean lineage Lara in Adl et al. 2019. Achlya Nees 1823; Aphanomyces de Bary 1860; Aplanopsis Höhnk 1952; Apodachlya Pringsh. 1883; Aquastella S.L.Glockling & D.P. Molloy 2014; Geolegnia Coker & J.V.Harv. 1925; Leptomitus (Roth) C.Agardh 1824; Newbya M.W.Dick & M.A.Spencer 2002; Pythiopsis de Bary 1888; Protoachlya Cocker 1923; Salisapilia Hulvey, Nigrelli, Telle, Lamour & Thines 2010; Saprolegnia Nees 1823; Thraustotheca Humphrey 1893.
    • Peronosporalean lineage Lara in Adl et al. 2019. Albugo (Pers.) Roussel ex Gray 1821; Bremia Regel 1843; Chlamydomyzium M.W.Dick 1997; Halophytopthora H.H.Ho & S.C.Jong 1990; Hyaloperonospora Constant. in Constant. & J.Fatehi 2002; Lagenidium Zopf 1859; Myzocytiopsis M.W.Dick 1997; Peronospora Corda 1837; Plasmopara J.Schröt. 1886; Pythium Pringsh. 1858; Pseudoperonospora Rostovzez 1903; Phytophthora de Bary 1975; Phytopythium Abad, De Cock, Bala, Robideau, A.M.Lodhi & Lévesque in Bala et al. 2010; Pustula Thines 2005.
• Subphylum/Division Ochrophyta Cavalier-Smith 1986, emend. Cavalier-Smith & Chao 1996 (=Heterokontophyta Guiry, R.A.Andersen & Moestrup 2023). Incertae sedis genera: Commation Thomsen & Larsen 1993.^[p]
  • Order Actinophryida^? Claus 1874, emend. Hartmann 1926^[p]
    • Suborder Actinosphaerina Cavalier-Smith 2013 → family Actinosphaeriidae Cavalier-Smith 2013. Sole genus: Actinosphaerium Ritter von Stein 1857 (=Echinosphaerium Hovasse 1965).
    • Suborder Actinophryina Cavalier-Smith 2013
      • Family Actinophryidae Dujardin 1841. Sole genus: Actinophrys Ehrenberg 1830 (=Trichoda Müller 1773 nomen oblitum, Peritricha Bory de St.Vincent 1824 nomen dubium).
      • Family Helioraphidae Cavalier-Smith 2013. Sole genus: Heliorapha Cavalier-Smith 2013.
  • Infraphylum Chrysista Cavalier-Smith 1986. Incertae sedis genera: Chrysoderma C.Billard 1984 nom. inval.; Chrysomeris Carter 1937; Chrysonephos W.R.Taylor 1952; "Giraudyopsis" Dangeard 1965 nom. inval.;^[82] Rhamnochrysis Wilce & Markey 1974.^[q]
    • Class Eustigmatophyceae^? Hibberd & Leedale 1971^[86][r]
      • Clade Goniochloridales K.P.Fawley, M.Eliáš & M.W.Fawley 2013. Genera: Goniochloris Geitler 1928; Pseudostaurastrum Chodat 1921; Tetraedriella Pascher 1930 nom. cons.; Trachydiscus H.Ettl 1964; Trebonskia Přibyl & Procházková 2022;^[88] Vacuoliviride Nakayama, Nakamura, Yokoyama, Shiratori, Inouye & Ishida 2015.
      • Order Eustigmatales Hibberd 1981
        • Paraeustigmatos M.W.Fawley, Nĕmcová & K.P.Fawley 2019^[89]
        • Family Eustigmataceae Hibberd 1981. Genera: Ellipsoidion Pascher 1938; Chlorobotrys Bohlin 1901; Eustigmatos Hibberd 1981; Pseudocharaciopsis K.W.Lee & Bold 1973; Vischeria Pascher 1938.
        • Family Monodopsidaceae Hibberd 1981 (includes Loboceae Hedgewald in Hedgewald, Padisak & Friedl 2007). Genera: Microchloropsis M.W.Fawley, I.Jameson & K.P.Fawley 2015; Monodopsis Hibberd 1981; Nannochloropsis Hibberd 1981; Pseudotetraedriella Hedgewald in Hedgewald, Padisak & Friedl 2007.
        • Family Neomonodaceae R.Amaral, K.P.Fawley, Nĕmcová, T.Ševčíková, Lukešová, M.W.Fawley, L.M.A.Santos & M.Eliáš 2020. Genera: Botryochloropsis^? Preisig & Wilhelm 1989; Characiopsella R.Amaral, K.P.Fawley, Nĕmcová, T.Ševčíková, Lukešová, M.W.Fawley, L.M.A.Santos & M.Eliáš 2020; Munda R.Amaral, K.P.Fawley, Nĕmcová, T.Ševčíková, Lukešová, M.W.Fawley, L.M.A.Santos & M.Eliáš 2020; Neomonodus R.Amaral, K.P.Fawley, Nĕmcová, T.Ševčíková, Lukešová, M.W.Fawley, L.M.A.Santos & M.Eliáš 2020; Pseudellipsoidion (Neustupa & Nĕmcová) Nĕmcová emend. Amaral et al. 2020.
    • SII clade
      • Class Olisthodiscophyceae Barcytė, Eikrem & M. Eliáš 2021 → order Olisthodiscales Cavalier-Smith 2013 emend. Barcytė, Eikrem & M. Eliáš 2021 → family Olisthodiscaceae Cavalier-Smith 2013 emend. Barcytė, Eikrem & M. Eliáš 2021.^[90] Sole genus: Olisthodiscus Carter 1937.
      • Class Pinguiophyceae Kawachi, Inouye, Honda, O'Kelly, Bailey, Bidigare & R.A.Andersen 2002 → order Pinguiochrysidales Kawachi, Inouye, Honda, O'Kelly, Bailey, Bidigare & R.A.Andersen 2002 → family Pinguiochrysidaceae Kawachi, Inouye, Honda, O'Kelly, Bailey, Bidigare & R.A.Andersen 2002. Genera: Glossomastix O'Kelly 2002; Phaeomonas Honda & Inouye 2002; Pinguiochrysis Kawachi 2002; Pinguiococcus R.A.Andersen, D.Potter & J.C.Bailey 2002; Polypodochrysis Magne 1975.
      • SSC clade^[87][81]
        • Chrysophyceae Pascher 1914. Incertae sedis taxa: Chryososaccus, Chrysosphera, Cyclonexis, Lygynion, Phaeoplaca.
          • Chromulinales Pascher 1910. Chromulina, Chrysomonas.
          • Hibberdiales Andersen 1989. Hibberdia.
          • Ochromonadales Pascher 1910. Spumella, Pedospumella, Ochromonas.
          • Paraphysomonadida Scoble & Cavalier-Smith 2014. Paraphysomonas.
          • Synurales Andersen 1987. Chrysodidymus, Mallomonas, Synura, Tesselaria.
        • Picophagea Cavalier-Smith 2006 emend. 2017^[74] [Synchromophyceae S.Horn & C.Wilhelm 2007]. Chlamydomyxa, Chrysopodocystis, Guanochroma, Leukarachnion, Picophagus, Synchroma.
    • SI clade^[85]/PXR clade^[87][81]
      • Class Raphidophyceae Chadefaud 1950 ex Silva 1980 → order Chattonellales Throndsen in Tomas 1993 emend. Yamaguchi, Nakayama, Murakami & Inouye 2010 (=Vacuolariales Shameel, 2001). Genera: Chattonella, Fibrocapsa, Goniostomum, Haramonas, Heterosigma, Merotricha, Vacuolaria.
      • PX clade^[85]
        • Class Chrysoparadoxophyceae Wetherbee in Wetherbee et al. 2019 → order Chrysoparadoxales Wetherbee in Wetherbee et al. 2019 → family Chrysoparadoxaceae Wetherbee in Wetherbee et al. 2019.^[91] Genera: Chrysoparadoxa Wetherbee in Wetherbee et al. 2019; Nematochrysis^? Pascher 1925 (=Chrysowaernella Gayral & Lepailleur 1971).^[85]
        • Phaeophyceae Hansgirg 1886 [Kjellman 1891; Pfitzer 1894]
          • Ascoseirales Petrov 1964. Ascoseira.
          • Desmarestiales Setchell & Gardner 1925. Arthrocladia, Desmarestia (P), Himantothallus, Phaeurus.
          • Dictyotales Bory de Saint-Vincent 1828. Dictyota, Dilophus, Lobophora, Padina, Stypopodium, Taonia, Zonaria.
          • Discosporangiales Kawai et al. 2007. Choristocarpus, Discosporangium.
          • Ectocarpales Bessey 1907, emend. Silva & Reviers 2000. Adenocystis, Acinetospora, Asterocladon, Asteronema, Chordaria, Ectocarpus, Scytosiphon.
          • Fucales Bory de Saint-Vincent 1927. Ascophyllum, Bifurcaria, Cystoseira, Druvillaea, Fucus, Hormosira, Sargassum, Turbinaria.
          • Ishigeales Cho et al. 2004 [Ishigeacea Okamura 1935]. Ishige.
          • Laminariales Migula 1908. Akkesiophycus, Alaria, Chorda, Costaria, Laminaria, Lessonia, Pseudochoda.
          • Nemodermatales Parente et al. 2008. Nemoderma.
          • Onslowiales Draisma & Prud'homme van Reine 2008. Onslowia.
          • Ralfsiales Nakamura ex Lim & Kawai 2007. Lithoderma, Neoralfsia, Pseudolithoderma, Ralfsia.
          • Scytothamnales Peters & Clayton 1998. Scytothamnus, Splachnidium, Stereocladon.
          • Sphacelariales Migula 1908. Chaetopteris, Halopteris, Stypocaulon, Sphacelaria, Verosphacella.
          • Sporochnales Sauvageau 1926. Bellotia, Carpomitra, Nereia, Sporochonus, Tomaculopsis.
          • Syringodermatales Henry 1984. Syringoderma.
          • Tilopteridales Bessey 1907. Cutleria, Halosiphon, Haplospora, Phaeosiphoniella, Phyllaria, Tilopteris.
        • Class Phaeosacciophyceae R.A.Andersen, L.Graf & H.S.Yoon in Graf et al. 2020 → order Phaeosacciales R.A.Andersen, L.Graf & H.S.Yoon in Graf et al. 2020^[85]
          • Family Phaeosaccionaceae J. Feldmann 1949. Genera: Antarctosaccion Delépine 1970; Phaeosaccion Farlow 1882.
          • Family Tetrasporopsidaceae R.A.Andersen, L.Graf & H.S.Yoon in Graf et al. 2020. Genera: Tetrasporopsis Lemmermann 1899; Psammochrysis R.Wetherbee in Graf et al. 2020.
        • Phaeothamniophyceae Andersen & Bailey in Bailey et al. 1998
          • Phaeothamniales Bourrelly 1954, emend. Andersen & Bailey in Bailey et al. 1998. Phaeothamnion.
          • Pleurochloridales Ettl 1956. Pleurochloridella.
        • Schizocladiophyceae Henry, Okuda & Kawai 2003. Schizocladia.
        • Xanthophyceae Allorge 1930, emend. Fritsch 1935 [Heterokontae Luther 1899; Heteromonadea Leedale 1983; Xanthophyta Hibberd 1990]
          • Tribonematales Pascher 1939. Botrydium, Bumilleriopsis, Characiopsis, Chloromeson, Heterococcus, Monadus, Ophiocytium, Sphaerosorus, Tribonema, Xanthonema.
          • Vaucheriales Bohlin 1901. Vaucheria.
  • Diatomista Derelle et al. 2016, emend. Cavalier-Smith 2017 [SIII clade]. Incertae sedis taxa: environmental clades MOCH-1, MOCH-2 and MOCH-4 Massana et al. 2014.
    • Bolidophyceae Guillou et al. 1999 [Parmales Booth & Marchant 1987]. Bolidomonas, Triparma, Tetraparma, Pentalamina.
    • Diatomeae Dumortier 1821 [Bacillariophyta Haeckel 1878]
      • Leptocylindrophytina D.G. Mann, in Adl et al. 2019
        • Leptocylindrophyceae D.G. Mann, in Adl et al. 2019. Leptocylindrus, Tenuicylindrus.
        • Corethrophyceae D.G. Mann, in Adl et al. 2019. Corethron.
      • Ellerbeckiophytina D.G. Mann, in Adl et al. 2019. Ellerbeckia.
      • Probosciophytina D.G. Mann, in Adl et al. 2019. Proboscia.
      • Melosirophytina D.G. Mann, in Adl et al. 2019. Aulacoseira, Melosira, Hyalodiscus, Stephanopyxis, Paralia, Endictya.
      • Coscinodiscophytina Medlin & Kaczmarska 2004, emend. Adl et al. 2019. Actinoptychus, Coscinodiscus, Actinocyclus, Asteromphalus, Aulacodiscus, Stellarima.
      • Rhizosoleniophytina D.G. Mann, in Adl et al. 2019. Guinardia, Rhizosolenia, Pseudosolenia.
      • Arachnoidiscophytina D.G. Mann, in Adl et al. 2019. Arachnoidiscus.
      • Bacillariophytina Medlin & Kaczmarska 2004, emend. Adl et al. 2019
        • Mediophyceae Jouse & Proshkina-Lavrenko in Medlin & Kaczmarska 2004
          • Chaetocerotophycidae Round & R.M. Crawford in Round et al. 1990, emend. Adl et al. 2019. Chaetoceros, Bacteriastrum, Dactyliosolen, Cerataulina, Hemiaulus, Eucampia, Acanthoceras, Urosolenia, Terpsinoë, Hydrosera.
          • Lithodesmiophycidae Round & R.M. Crawford in Round et al. 1990, emend. Adl et al. 2019. Lithodesmium, Lithodesmioides, Helicotheca, Bellerochea, Ditylum.
          • Thalassiosirophycidae Round & R.M. Crawford in Round et al. 1990. Thalassiosira, Lindavia, Cyclotella, Stephanodiscus, Cyclostephanos, Discostella, Bacteriosira, Skeletonema, Detonula.
          • Cymatosirophycidae Round & R.M. Crawford in Round et al. 1990. Cymatosira, Minutocellus, Papiliocellulus, Leyanella, Extubocellulus, Plagiogrammopsis, Campylosira, Brockmanniella, Pierrecomperia.
          • Odontellophycidae D. G. Mann, in Adl et al. 2019. Odontella, Triceratium, Cerataulus, Pleurosira, Pseudauliscus, Amphitetras, Trieres, Mastodiscus.
          • Chrysanthemodiscophycidae D.G. Mann, in Adl et al. 2019. Chrysanthemodiscus, Biddulphiopsis, Trigonium, Isthmia, Lampriscus, Stictocyclus, Ardissonea, Climacosphenia, Toxarium.
        • Biddulphiophyceae D. G. Mann, in Adl et al. 2019
          • Biddulphiophycidae Round and R.M. Crawford in Round et al. 1990, emend. Adl et al. 2019. Biddulphia.
          • Attheya T. West 1860
        • Bacillariophyceae Haeckel 1878, emend. Adl et al. 2019
          • Striatellaceae Kützing 1844. Striatella, Pseudostriatella.
          • Urneidophycidae Medlin 2016. (P?) Plagiogramma, Dimeregramma, Rhaphoneis, Delphineis, Psammoneis, Bleakeleya, Asterionellopsis.
          • Fragilariophycidae Round in Round, Crawford & Mann 1990, emend. Adl et al. 2019. Fragilaria, Synedra, Tabellaria, Asterionella, Diatoma, Tabularia, Cyclophora, Astrosyne, Licmophora, Rhabdonema, Grammatophora, Staurosira, Thalassionema.
          • Bacillariophycidae D.G. Mann in Round, Crawford & Mann 1990, emend. Adl et al. 2019. Eunotia, Achnanthes, Bacillaria, Nitzschia, Pseudonitzschia, Cylindrotheca, Navicula, Seminavis, Haslea, Pleurosigma, Gyrosigma, Achnanthidium, Cocconeis, Frustulia, Diploneis, Sellaphora, Pinnularia, Gomphonema, Cymbella, Didymosphenia, Phaeodactylum, Amphora, Entomoneis, Epithemia, Surirella, etc.
            • Naviculales Bessey 1907
              • Stauroneidaceae D.G. Mann in Round, Crawford & Mann 1990. Craticula, Dorofeyukea, Fistulifera, Karayevia, Madinithidium, Parlibellus, Prestauroneis, Stauroneis, Schizostauron.^[92]
    • Dictyochophyceae Silva 1980 [Silicoflagellata Lemmermann, 1901]
      • Dictyochales Haeckel 1894 [Dictyochida Borgert, 1891; Dictyochaceae Lemmermann, 1901]. Dictyocha.
      • Florenciellales Eikrem, Edvardsen & Throndsen 2007.^[93] Florenciella, Verrucophora.
      • Pedinellales Zimmermann et al. 1984 [Ciliophryida Febre-Chevalier, 1985; Actinomonadaceae Kent, 1880]. Actinomonas, Apedinella, Ciliophrys, Mesopedinella, Palatinella, Pedinella, Pseudopedinella, Pteridomonas.
      • Rhizochromulinales O'Kelly & Wujek 1994 [Rhizochromulinaceae O'Kelly & Wujek, 1994]. Rhizochromulina.
    • Pelagophyceae Andersen & Saunders 1993
      • Pelagomonadales Andersen & Saunders 1993. Aureococcus, Pelagococcus, Pelagomonas.
      • Sarcinochrysidales Gayral & Billard 1977
        • Sarcinochrysidaceae Gayral & Billard 1977. Ankylochrisis, Arachnochrysis, Aureoscheda, Aureoumbra, Nematochrysopsis, Pelagospilus, Pulvinaria, Sarcinochrysis, Sargassococcus.
        • Chrysocystaceae M.Melkonian, H.S.Yoon & R.A.Andersen 2018.^[94] Chrysocystis, Chrysoreinhardia, Sungminbooa.
      • Plocamiomonadales Daugbjerg & Lovejoy 2024. Plocamiomonas.^[95]

Alveolata Cavalier-Smith 1991

Myzozoa Apicomplexa Colpodellida Squirmida Perkinsozoa Dinoflagellata Neocolponema Palustrimonas Ciliophora Acavomonas Colponema Loeffela

Cladogram of Alveolata, based on a SSU rDNA phylogeny of basal alveolates[96] and a 203-gene phylogeny of apicomplexans and their relatives[97] published in 2023.

• Colponemida^(P) Cavalier-Smith 1993 emend. Adl et al. 2019 (=Protalveolata Cavalier-Smith 1991 emend. 2017. Genera not assigned to families: Neocolponema Gigeroff et al. 2023; Loeffela Gigeroff et al. 2023^[96]
  • Phylum^[s] Colponemidia Tikhonenkov et al. 2014 → class Colponemea Cavalier-Smith 1993 → order Colponemida Cavalier-Smith 1993 → family Colponemidae Cavalier-Smith & Chao 2004. Sole genus: Colponema Stein 1878.
  • Phylum^[s] Acavomonidia Tikhonenkov et al. 2014 → class Acavomonea Tikhonenkov et al. 2014 → order Acavomonida Tikhonenkov et al. 2014 → family Acavomonidae Tikhonenkov et al. 2014. Acavomonas Tikhonenkov et al. 2014.
  • Order Palustrimonadida Cavalier-Smith 2017 → family Palustrimonadidae Cavalier-Smith 2017. Sole genus: Palustrimonas Patterson & Simpson 1996.

Myzozoa Cavalier-Smith & Chao 2004

• Phylum^[s] Chromerida R.B.Moore et al. 2008 → class Colpodellophyceae Molinari & Guiry 2023^[98] ("chrompodellids")^[99] → order Colpodellales^ICN/Colpodellida^ICZN Cavalier-Smith 1993 emend. Adl et al. 2005, 2019. Incertae sedis genus: Piridium Patten 1936.^[100]
  • Family Vitrellaceae Oborník & Lukeš 2011. Sole genus: Vitrella Oborník & Lukeš 2011.
  • Family Colpodellaceae Adl et al. 2019. Genera: Colpodella Cienkowsky 1865; Chilovora Cavalier-Smith 2004; Voromonas Cavalier-Smith 2004.
  • Family Chromeraceae Oborník & Lukeš 2012. Sole genus: Chromera R.B.Moore et al. 2008.
  • Family Alphamonadaceae^ICN/Alphamonadidae^ICZN Cavalier-Smith in Cavalier-Smith & Chao 2004. Sole genus: Alphamonas Aléxéieff 1918.
• Phylum^[s] Perkinsozoa Norén & Moestrup in Norén et al 1999 → class Perkinsea Levine 1978. Incertae sedis genera: Phagodinium Kristiansen 1993; Rastrimonas Brugerolle 2003;^[t] Acrocoelus Fernández, Pardos, Benito & Arroyo 1999.
  • Maranthos Alacid & Reñé 2021^[105]
  • Family Pararosariidae Jeon & Park 2021. Sole genus: Pararosarium Jeon & Park 2021.^[106]
  • Family Parviluciferaceae Reñé & Alacid 2017. Genera: Dinovorax Reñé & Alacid 2017; Parvilucifera Norén & Moestrup 1999; Snorkelia Reñé & Alacid 2017;^[107] Tuberlatum Jeon & Park 2019.^[108]
  • Family Perkinsidae Levine 1978. Sole genus: Perkinsus Levine 1978.
  • Family Xcellidae Freeman, Fuss, Kristmundsson, Keeling, Shalchian-Tabrizi & Bass 2017 em. Karlsbakk, Nystøyl, Plarre & Nylund 2021. Genera: Cryoxcellia Evans, Patel, Matzke & Millar 2023,^[109] Gadixcellia Freeman, Fuss, Kristmundsson, Keeling, Shalchian-Tabrizi & Bass 2017; Notoxcellia Desvignes et al. 2022;^[110] Salmoxcellia Karlsbakk, Nystøyl, Plarre & Nylund 2021;^[111] Xcellia Freeman, Fuss, Kristmundsson, Keeling, Shalchian-Tabrizi & Bass 2017.
• Phylum^[s] Dinoflagellata Bütschli 1885, emend. Fensome et al. 1993, emend. Adl et al. 2005. Incertae sedis genera: free-living (Adenoides, Akashiwo, Amphidiniella, Ankistrodinium, Apicoporus, Archaeosphaerodiniopsis, Bispinodinium, Bysmatrum, Cabra, Cladopyxis, Crypthecodinium, Cucumeridinium, Dactylodinium, Dicroerisma, Gloeodinium, Grammatodinium, Gynogonadinium, Gyrodiniellum, Halostylodinium, Heterodinium, Moestrupia, Paragymnodinium, Phytodinium, Plagiodinium, Planodinium, Pileidinium, Pseudadenoides, Pseudothecadinium, Pyramidodinium, Rhinodinium, Roscoffia, Sabulodinium, Sphaerodinium, Spiniferodinium, Testudodinium, Thecadinium, Thecadiniopsis, Togula) and parasitic Blastodiniales Chatton 1906 [no longer valid] (Amyloodinium, Apodinium, Cachonella, Caryotoma, Crepidoodinium, Haplozoon, Oodinium, Myxodinium, Piscinoodinium, Protoodinium, Rhinodinium, Schyzochitriodinium, Stylodinium).
  • Psammosa Okamoto, A. Horák & Keeling 2012^[112][113]
  • Family Oxyrrhinaceae Sournia 1984. Sole genus: Oxyrrhis Dujardin 1841.^[113]
  • Eleftheros Tikhonenkov, Hehenberger & Keeling 2023^[113]
  • Class Endodinea Cavalier-Smith 2017 → order Ichthyodinida Cavalier-Smith 2017 (environmental Marine Alveolate Group I)^[113]
    • Family Hobagellidae Yoo, Kim & Wayne Coats 2024. Sole genus: Hobagella Yoo, Kim & Wayne Coats 2024.^[114]
    • Family Euduboscquellidae Coats & Bachvaroff 2012. Euduboscquella D.W.Coats, T.R.Bachvaroff & C.F.Delwiche 2012; Dogelodinium Loeblich & A.R.Loeblich 1966 nom. cons.; Keppenodinium Loeblich & A.R.Loeblich 1966 nom. cons. (=Hollandella Cachon 1964).
    • Family Ichthyodiniidae Cavalier-Smith 2017. Sole genus: Ichthyodinium Hollande & Cachon 1952.
  • Class Ellobiopsea A.R.Loeblich 1976 → order Ellobiopsida Whisler 1990 → family Ellobiopsidae Coutière 1911. Genera: Ellobiopsis Caullery 1910; Thalassomyces Niezabitowski 1913; Parallobiopsis^? B.Collin 1913; Ellobiocystis^? Coutière 1911; Rhizellobiopsis^? Hovasse 1926.^[u]
  • Class Syndiniophyceae^ICN/Syndinea^ICZN A.R.Loeblich 1976 → order Syndiniales A.R.Loeblich 1976
    • Family Amoebophryaceae^ICN/Amoebophryidae^ICZN Cachon 1964 (environmental Marine Alveolate Group II). Sole genus: Amoebophrya Koeppen 1892.
    • Family Syndiniaceae^ICN/Syndinidae^ICZN Chatton 1910 (environmental Marine Alveolate Group IV). Hematodinium, Syndinium, Solenodinium.
    • Family Sphaeriparaceae A.R.Loeblich 1970. Genera: Atlanticellodinium J.Cachon & M.Cachon-Enjumet 1965; Sphaeripara Poche 1911 nom. cons.
  • Class Noctiluciphyceae Fensome et al. 1993→ order Noctilucales Haeckel 1894. Abedinium, Cachonodinium, Craspedotella, Cymbodinium, Kofoidinium, Leptodiscus, Noctiluca, Petalodinium, Pomatodinium, Scaphodinium, Spatulodinium.
  • Class Dinophyceae Pascher 1914
    • Subclass Gymnodiniphycidae Fensome et al. 1993
      • Gymnodiniales F. Stein 1878, emend. G. Hansen & Moestrup in Daugbjerg et al. 2000 sensu stricto. Barrufeta, Chytriodinium, Dissodinium, Erythropsidinium, Greuetodinium, Gymnodinium, Lepidodinium, Nematodinium, Nusuttodinium, Pellucidodinium, Polykrikos, Proterythropsis, Wangodinium,^[116] Warnowia.
      • Amphidinium Claparède & Lachmann 1859, emend. Flø Jørgensen et al. 2004 sensu stricto
      • Gyrodinium Kofoid & Swezy 1921, emend. G. Hansen & Moestrup in Daugbjerg et al. 2000 sensu stricto
      • Kareniaceae Bergholtz et al. 2005. Brachidinium, Karenia, Karlodinium, Takayama.
      • Ceratoperidiniaceae Loeblich III 1980, emend. Reñé & de Salas 2013. Ceratoperidinium, Kirithra.
      • Torodiniales Boutrup, Moestrup & Daugbjerg 2016. Kapelodinium, Torodinium.
      • Levanderina Moestrup et al. 2014
      • Margalefidinium F. Gómez, Richlen & D.M. Anderson 2017
      • Cochlodinium F. Schütt emend. F. Gómez, Richlen & D.M. Anderson 2017 sensu stricto
      • Ptychodiscales Fensome et al. 1993. Achradina, Amphilothus, Balechina, Ptychodiscus, Sclerodinium.
      • Borghiellaceae Moestrup, Lindberg, & Daugbjerg 2009. Baldinia, Borghiella.
      • Tovelliaceae Moestrup et al. 2005. Bernardinium, Esoptrodinium, Jadwigia, Tovellia.
      • Suessiaceae Fensome et al. 1993, emend. Moestrup et al. 2009. Ansanella, Asulcocephalium, Biecheleria, Biecheleriopsis, Leiocephalium, Pelagodinium, Polarella, Prosoaulax, Protodinium, Symbiodinium, Yihiella.
    • Subclass Peridiniphycidae Fensome et al. 1993
      • Gonyaulacales Taylor 1980. Alexandrium, Amylax, Ceratium, Ceratocorys, Coolia, Fukuyoa, Fragilidium, Gambierdiscus, Goniodoma, Gonyaulax, Lingulodinium, Ostreopsis, Pentaplacodinium, Peridiniella, Protoceratium, Pyrocystis, Pyrodinium, Pyrophacus, Tripos.
      • Peridiniales Haeckel 1894. Amphidiniopsis, Archaeperidinium, Blastodinium*, Diplopelta, Diplopsalis, Diplopsalopsis, Herdmania, Niea, Oblea, Palatinus, Parvodinium, Peridinium, Peridiniopsis, Preperidinium, Protoperidinium, Qia, Vulcanodinium.
      • Thoracosphaeraceae Schiller 1930. Aduncodinium, Amyloodinium, Apocalathium, Blastodinium, Chimonodinium, Cryptoperidiniopsis, Duboscquodinium, Ensiculifera, Laciniporus,^[117] Leonella, Luciella, Naiadinium, Paulsenella, Pentapharsodinium, Pfiesteria, Scrippsiella, Stoeckeria, Theleodinium, Thoracosphaera, Tintinnophagus, Tyrannodinium.
      • Podolampadaceae Lindemann 1928. Blepharocysta, Gaarderiella, Heterobractum, Lissodinium, Mysticella, Podolampas.
      • Kryptoperidiniaceae Lindemann 1925 ["dinotoms"]. Blixaea, Durinskia, Galeidinium, Kryptoperidinium, Unruhdinium, etc.
      • Heterocapsaceae Fensome et al. 1993. Heterocapsa.
      • Amphidomataceae Sournia 1984. Amphidoma, Azadinium.
      • Oxytoxaceae Lindemann 1928. Corythodinium, Oxytoxum.
      • Centrodiniaceae Hernández-Becerril 2010. Centrodinium.
    • Dinophysales Kofoid 1926. Amphisolenia, Citharistes, Dinofurcula, Dinophysis, Histioneis, Latifascia, Metadinophysis, Metaphalacroma, Ornithocercus, Oxyphysis, Parahistioneis, Phalacroma, Pseudophalacroma, Sinophysis, Triposolenia.
    • Prorocentrales Lemmermann 1910. Mesoporus, Prorocentrum.
• Class Squirmidea Cavalier-Smith 2014. Digyalum, Filipodium, Platyproteum.^[118][119]
• Phylum^[s] Apicomplexa Levine 1980, emend. Adl et al. 2005. Incertae sedis genera: Aggregata^[v] Frenzel 1885, Christalloidophora Dehorne 1934, Dobellia* Ikeda 1914, Echinococcidium* Porchet 1978, Globidiellum* Brumpt 1913, Joyeuxella* Brasil 1902, Rhabdospora* Laguesse 1906, Spermatobium* Eisen 1895, Spiriopsis* Arvy & Peters 1972, Spirogregarina* Wood & Herman 1943, Toxocystis* Léger & Duboscq 1910, Trophosphaera* Le Calvez 1939.
  • Order Agamococcidiorida^? Levine 1979 (=Histogregarida Cavalier-Smith 2014)
    • Family Gemmocystidae Upton & Peters 1986. Sole genus: Gemmocystis.
    • Family Rhytidocystidae Levine 1979. Sole genus: Rhytidocystis.
  • Order Protococcidiorida^? Kheisin 1956 (=Coelotrophiida Vivier 1982). Angeiocystis*, Coelotropha*, Grellia*, Eleutheroschizon*, Mackinnonia*, Myriosporides*, Myriospora*, Sawayella*.
  • Aconoidasida^(P) Mehlhorn, Peters & Haberkorn 1980 (=Hematozoa Vivier 1982)
    • Order Haemospororida Danielewsky 1885. Dionisia*, Haemocystidium, Haemoproteus, Hepatocystis, Leucocytozoon, Mesnilium*, Nycteria, Parahaemoproteus, Plasmodium, Polychromophilus, Rayella*, Saurocytozoon*.
    • Order Piroplasmida Wenyon 1926. Anthemosoma*, Babesia, Cytauxzoon, Echinozoon*, Haemohormidium*, Sauroplasma*, Serpentoplasma*, Theileria.
    • Order Nephromycida Cavalier-Smith 1993, emend. Adl et al. 2019. Nephromyces, Cardiosporidium.
  • Conoidasida^(P) Levine 1988
    • Order Corallicolida Kwong et al. 2021 → family Corallicolidae Kwong et al. 2021. Genera: Corallicola Kwong et al. 2021; Anthozoaphila Kwong et al. 2021; Gemmocystis Upton & Peters 1986.^[121]
    • Coccidia Leuckart 1879 (P)
      • Suborder Adeleorina Léger 1911. Adelea*, Adelina, Babesiosima*, Bartazoon*, Chagasella*, Cyrilia*, Dactylosoma, Desseria*, Ganapatiella*, Gibbsia*, Haemogregarina, Haemolivia, Hepatozoon, Ithania*, Karyolysus, Klossia, Klossiella*, Legerella*, Orcheobius*, Rasajeyna*.
      • Suborder Eimeriorina Léger 1911. Atoxoplasma, Barrouxia*, Besnoitia, Caryospora, Caryotropha, Choleoeimeria, Cyclospora, Cystoisospora, Defretinella*, Diaspora*, Dorisa*, Dorisiella*, Eimeria, Elleipsisoma*, Goussia, Hammondia, Hyaloklossia, Isospora, Lankesterella, Mantonella*, Merocystis, Neospora, Nephroisospora, Ovivora*, Pfeifferinella, Pseudoklossia, Sarcocystis, Schellackia, Selenococcidium*, Selysina*, Spirocystis*, Toxoplasma, Tyzzeria*, Wenyonella*.
    • Gregarinida Dufour 1828. Incertae sedis taxa: Digyalum Koura et al. 1990, Exoschizon Hukui 1939.
      • Archigregarinorida Grassé 1953 (P). Meroselenidium, Merogregarina, Selenidium, Selenocystis, Veloxidium.
      • Eugregarinorida Léger 1900 (P). Apolocystis*, Amoebogregarina, Ancora, Ascogregarina, Asterophora, Blabericola, Caliculium, Cephaloidophora, Colepismatophila, Cystobia*, Cystocephalus*, Difficilina, Diplauxis*, Enterocystis, Ganymedes, Geneiorhynchus, Gonospora, Gregarina, Heliospora, Hentschelia*, Hirmocystis*, Hoplorhynchus, Lankesteria, Lecudina, Leidyana, Lithocystis, Monocystella*, Monocystis, Nematopsis, Nematocystis*, Neoasterophora*, Paralecudina, Paraschneideria, Phyllochaetopterus, Pileocephalus*, Polyplicarium, Polyrhabdina, Porospora*, Prismatospora, Protomagalhaensia, Psychodiella, Pterospora, Pyxinia, Pyxinioides, Rhabdocystis*, Sphaerorhynchus*, Steinina, Stenophora, Stylocephalus, Sycia*, Syncystis, Thalicola*, Thiriotia, Trichotokara, Uradiophora*, Urospora, Xiphocephalus, Zygosoma*, and more.
      • Neogregarinorida Grassé 1953. Apicystis, Aranciocystis, Caulleryella*, Coelogregarina*, Farinocystis*, Gigaductus*, Lipocystis*, Lipotropha*, Lymphotropha*, Machadoella*, Mattesia, Menzbieria, Ophryocystis, Schizocystis*, Syncystis, Tipulocystis*.
      • Cryptogregarinorida Cavalier-Smith 2014, emend. Adl et al. 2019. Cryptosporidium.
    • Class Blastogregarinea Chatton and Villeneuve 1936, emend. Simdyanov et al. 2018. Chattonaria, Siedleckia.

Phylum Ciliophora Doflein 1901

• Postciliodesmatophora Gerassimova & Seravin 1976
  • Karyorelictea Corliss 1974
    • Kentrophoridae Jankowski 1980. Kentrophoros.
    • Loxodida Jankowski 1980
      • Cryptopharyngidae Jankowski 1980. Cryptopharynx.
      • Loxodidae Bütschli 1889. Loxodes.
    • Geleiidae Kahl 1933. Geleia.
  • Heterotrichea Stein 1859
    • Blepharismidae Jankowski in Small & Lynn 1985. Blepharisma
    • Climacostomidae Repak 1972. Climacostomum.
    • Condylostomatidae Kahl in Doflein & Reichenow 1929. Chattonidium, Condylostoma.
    • Fabreidae Shazib et al. 2014. Fabrea.
    • Gruberiidae Shazib et al. 2014. Gruberia.
    • Coliphorina Jankowski 1967
      • Folliculinidae Dons 1914. Folliculina.
      • Maristentoridae Miao et al. 2005. Maristentor.
    • Peritromidae Stein 1867. Peritromus.
    • Spirostomidae Stein 1867. Anigsteinia, Spirostomum.
    • Stentoridae Carus 1863. Stentor.
• Intramacronucleata Lynn 1996. Incertae sedis taxa: Protocruziidae Jankowski 1980 [Protocruziidia de Puytorac et al. 1987] (Protocruzia Faria da Cunha & Pinto 1922).
  • SAL Gentekaki et al. 2014. Incertae sedis taxa: Cariacotrichea Orsi et al. 2011 (Cariacothrix caudata), Mesodiniidae ankowski, 1980 (Mesodinium), Phacodiniidia Small and Lynn 1985 (Phacodinium).
    • Spirotrichea Bütschli 1889
      • Euplotia Jankowski 1979
        • Euplotida Small & Lynn 1985
          • Aspidiscidae Ehrenberg 1830. Aspidisca.
          • Certesiidae Borror & Hill 1995. Certesia.
          • Euplotidae Ehrenberg 1838. Euplotes.
          • Gastrocirrhidae Fauré-Fremiet 1961. Gastrocirrhus.
          • Uronychidae Jankowski 1975. Diophrys, Uronychia.
        • Discocephalida
          • Discocephalidae Jankowski 1979. Discocephalus, Prodiscocephalus, Paradiscocephalus.
          • Pseudoamphisiellidae Song et al. 1997. Leptoamphisiella, Pseudoamphisiella.
      • Perilemmaphora Berger 2008
        • Hypotrichia Stein 1859
          • Stichotrichida Fauré-Fremiet 1961 (P)^[w]
            • Amphisiellidae Jankowski 1979. Amphisiella, Bistichella.
            • Atractosidae Bourland 2015. Atractos.
            • Epiclintidae Wicklow & Borror 1990. Epiclintes.
            • Gonostomatidae Small & Lynn 1985. Cotterillia, Gonostomum.
            • Halteriidae Claparède & Lachmann 1858. Halteria, Meseres.
            • Holostichidae Fauré-Fremiet 1961. Holosticha, Uncinata.
            • Kahliellidae Tuffrau 1979. Deviata, Kahliella.
            • Keronidae Dujardin 1840. Kerona.
            • Oxytrichidae Ehrenberg 1830 (P). Cyrtohymena, Gastrostyla, Oxytricha, Stylonychia.
            • Parabirojimidae Dai & Xu 2011. Parabirojimia, Tunicothrix.
            • Plagiotomidae Bütschli 1887. Plagiotoma.
            • Psammomitridae Jankowski 1979. Psammomitra.
            • Pseudoamphisiellidae Song et al. 1996. Pseudoamphisiella.
            • Psilotrichidae Bütschli 1889. Psilotricha, Urospinula.
            • Schmidingerotrichidae Foissner 2012. Schmidingerothrix.
            • Spirofilidae von Gelei 1929. Spirofilopsis, Strongylidium.
            • Trachelostylidae Small & Lynn 1985. Trachelostyla.
            • Uroleptidae Foissner & Stoeck 2008. Paruroleptus, Uroleptus.
          • Urostylida Jankowski 1979 (P)
            • Bergeriellidae Liu et al. 2010. Bergeriella, Neourostylopsis.
            • Hemicycliostylidae Lyu et al. 2018. Australothrix, Hemicycliostyla.
            • Pseudokeronopsidae Borror & Wicklow, 1983. Apoholosticha, Pseudokeronopsis.
            • Pseudourostylidae Jankowski 1979. Pseudourostyla.
            • Urostylidae Bütschli 1889. Bakuella, Diaxonella, Urostyla.
        • Oligotrichea Bütschli 1887
          • Oligotrichida Bütschli 1887
            • Cyrtostrombidiidae Agatha 2004. Cyrtostrombidium.
            • Pelagostrombidiidae Agatha 2004. Pelagostrombidium.
            • Strombidiidae Fauré-Fremiet 1970. Strombidium (P).
            • Tontoniidae Agatha 2004. Laboea, Tontonia.
          • Choreotrichida Small & Lynn 1985. Incertae sedis taxa: Lynnella Liu et al. 2011 [Lynnellidae Liu et al. 2011; Lynnellida Liu et al. 2015]
            • Strobilidiina Jankowski 1980 (P)
              • Leegaardiellidae Lynn & Montagnes 1988. Leegaardiella.
              • Lohmanniellidae Montagnes & Lynn 1991. Lohmanniella.
              • Strobilidiidae Kahl in Doflein & Reichenow 1929. Strobilidium.
              • Strombidinopsidae Small & Lynn 1985. Strombidinopsis (P).
            • Tintinnina Kofoid & Campbell 1929. Incertae sedis taxa: Helicostomella, Tintinnopsis (P), several other genera.
              • Ascampbelliellidae Corliss 1960. Ascampbelliella
              • Cyttarocylididae Kofoid & Campbell 1929 [probably synonymous with Petalotrichidae]. Cyttarocylis.
              • Dictyocystidae Haeckel 1873. Dictyocysta.
              • Epiplocylididae Kofoid & Campbell 1939. Epiplocylis.
              • Eutintinnidae Bachy et al. 2012. Dartintinnus, Eutintinnus.
              • Favellidae Kofoid & Campbell 1929. Favella.
              • Nolaclusiliidae Sniezek et al. 1991. Nolaclusilis.
              • Petalotrichidae Kofoid & Campbell 1929 [probably synonymous with Cyttarocylididae]. Petalotricha.
              • Ptychocylididae Kofoid & Campbell 1929. Cymatocylis, Ptychocylis.
              • Rhabdonellidae Kofoid & Campbell 1929. Metacylis, Rhabdonella, Schmidingerella.
              • Stenosemellidae Campbell 1954 (P). Stenosemella.
              • Tintinnidae Claparède & Lachmann 1858. Amphorellopsis, Salpingacantha, Salpingella, Tintinnus.
              • Tintinnidiidae Kofoid & Campbell 1929. Tintinnidium.
              • Undellidae Kofoid & Campbell 1929. Undella.
              • Xystonellidae Kofoid & Campbell 1929. Dadayiella, Parafavella, Xystonella.
      • Licnophoridae Bütschli 1887. Licnophora, Prolicnophora.
      • Kiitrichidae Nozawa 1941. Caryotricha, Kiitricha.
    • Lamellicorticata Vd'ačný et al. 2010
      • Armophorea Lynn 2004. Incertae sedis taxa: Mylestomatidae Kahl in Doflein & Reichenow, 1929 (Mylestoma).
        • Metopida Jankowski 1980 (P)
          • Metopidae Kahl 1927 (P). Bothrostoma, Brachonella, Eometopus, Metopus, Parametopidium, Tesnospira.
          • Apometopidae Foissner 2016. Cirranter, Urostomides.
          • Tropidoatractidae Rotterová et al. 2018. Palmarella, Tropidoatractus.
        • Clevelandellida de Puytorac & Grain 1976
          • Clevelandellidae Kidder 1938. Clevelandella.
          • Inferostomatidae Ky 1971. Inferostoma.
          • Neonyctotheridae Affa'a 1987. Neonyctotherus.
          • Nyctotheridae Amaro 1972 (P). Nyctotherus.
          • Sicuophoridae Amaro 1972. Sicuophora.
        • Caenomorphidae Poche 1913. Caenomorpha, Ludio, Sulfonecta.
        • Odontostomatida Sawaya 1940
          • Discomorphellidae Corliss 1960. Discomorphella.
          • Epalxellidae Corliss 1960. Epalxella, Saprodinium.
      • Litostomatea Small & Lynn 1981
        • Rhynchostomatia Jankowski 1980
          • Dileptida Jankowski 1978
            • Dileptidae Jankowski 1980. Apodileptus, Dileptus, Pseudomonilicaryon.
            • Dimacrocaryonidae Jankowski 1978. Dimacrocaryon, Monomacrocaryon, Rimaleptus.
            • Tracheliidae Ehrenberg 1838. Trachelius.
        • Haptoria Corliss 1974 (P). Incertae sedis taxa: Chaenea.
          • Lacrymariidae de Fromentel 1876. Lacrymaria.
          • Haptorida Corliss 1974
            • Enchelyodonidae Foissner et al. 2002. Enchelyodon, Fuscheria.
            • Homalozoonidae Jankowski 1980. Homalozoon.
            • Pleuroplitidae Foissner 1996. Pleuroplites.
          • Didiniidae Poche 1913. Didinium, Monodinium.
          • Pleurostomatida Schewiakoff 1896
            • Amphileptidae Bütschli 1889. Amphileptus.
            • Litonotidae Kent 1882. Litonotus.
            • Kentrophyllidae Wu et al. 2015. Epiphyllum, Kentrophyllum.
          • Spathidiida Foissner & Foissner 1988
            • Acropisthiidae Foissner & Foissner 1988. Acropisthium, Chaenea.
            • Actinobolinidae Kahl 1930. Actinobolina.
            • Apertospathulidae Foissner et al. 2005. Apertospathula.
            • Enchelyidae Ehrenberg 1838. Enchelys.
            • Pseudoholophryidae Berger et al. 1984. Pseudoholophrya.
            • Spathidiidae Kahl in Doflein & Reichenow 1929. Legendrea,^[122] Spathidium.
            • Trachelophyllidae Kent 1882. Trachelophyllum.
          • Helicoprorodontidae Small & Lynn 1985
        • Trichostomatia Bütschli 1889
          • Vestibuliferida de Puytorac et al. 1974
            • Balantidiidae Reichenow in Doflein and Reichenow 1929. Balantidium, Neobalantidium (P).
            • Buetschliidae Poche 1913. Buetschlia.
            • Paraisotrichidae da Cunha 1917. Paraisotrichia.
            • Protocaviellidae Grain in Corliss 1979. Protocaviella.
            • Protohalliidae da Cunha & Muniz 1927. Protohallia.
            • Pycnotrichidae Poche 1913. Pycnothrix, perhaps Buxtonella.
        • Isoendo
          • Isotrichidae Bütschli 1889. Dasytricha, Isotricha.
          • Entodiniomorphida Reichenow in Doflein & Reichenow 1929
            • Blepharocorythina Wolska 1971
              • Blepharocorythidae Hsiung 1929. Blepharocorys.
              • Parentodiniidae Ito, Miyazaki & Imai 2002. Parentodinium.
              • Pseudoentodiniidae Wolska 1986. Pseudoentodinium.
            • Entodiniomorphina Reichenow in Doflein & Reichenow 1929
              • Cycloposthiidae Poche 1913. Cycloposthium.
              • Gilchristinidae Ito, Ishihara & Imai 2014 [Gilchristidae Ito et al. 2006]. Digilchristia, Gilchristina.^[123]
              • Ophryoscolecidae Stein 1859. Entodinium, Ophryoscolex, Polyplastron.
              • Polydiniellidae Corliss 1960. Polydiniella.
              • Rhinozetidae Van Hoven, Gilchrist & Hamilton-Attwell 1988. Rhinozeta.
              • Spirodiniidae Strelkow 1939. Spirodinium.
              • Telamodiniidae Latteur & Dufey 1967. Telamodinium.
              • Troglodytellidae Corliss 1979. Troglodytella,.
          • Macropodiniida Lynn 2008
            • Amylovoracidae Cameron & O'Donoghue 2002. Amylovorax.
            • Macropodiniidae Dehority 1996. Macropodinium.
            • Polycostidae Cameron & O'Donoghue 2003. Polycosta.
  • CONTHREEP Lynn in Adl et al. 2012 [Ventrata Cavalier-Smith 2004]. Incertae sedis taxa: Askenasia Blochmann 1895, Cyclotrichiidae Jankowski 1980 (Cyclotrichium), Paraspathidium Noland 1937, Pseudotrachelocercidae Song 1990 (Pseudotrachelocerca), Discotrichidae Jankowski 1967 [Discotrichida Fan et al. 2014] (Discotricha, Lopezoterenia).
    • Phyllopharyngea de Puytorac et al. 1974
      • Synhymeniida de Puytorac et al. in Deroux 1978
        • Nassulopsidae Deroux in Corliss 1979. Nassulopsis.
        • Orthodonellidae Jankowski 1968. Orthodonella, Zosterodasys.
        • Scaphidiodontidae Deroux in Corliss 1979. Chilodontopsis, Scaphidiodon.
        • Synhymeniidae Jankowski in Small & Lynn 1985. Synhymenia.
      • Subkinetalia Gong et al. 2009
        • Cyrtophoria Fauré-Fremiet in Corliss 1956
          • Chlamydodontida Deroux 1976 (P)
            • Chilodonellidae Deroux 1970. Chilodonella.
            • Chitonellidae Small & Lynn 1985. Chitonella.
            • Chlamydodontidae Stein 1859. Chlamydodon.
            • Gastronautidae Deroux 1994. Gastronauta.
            • Kryoprorodontidae Alekperov & Mamajeva 1992. Gymnozoum.
            • Lynchellidae Jankowski 1968. Chlamydonella, Lynchella.
          • Dysteriida Deroux 1976
            • Dysteriidae Claparède & Lachmann 1858. Dysteria (P), Trochilia.
            • Hartmannulidae Poche 1913 (P). Hartmannula.
            • Kyaroikeidae Sniezek & Coats 1996. Kyaroikeus.
            • Plesiotrichopidae Deroux 1976. Plesiotrichopus.
            • Chonotrichia Wallengren 1895
              • Exogemmida Jankowski 1972
                • Chilodochonidae Wallengren 1895. Chilodochona.
                • Filichonidae Jankowski 1973. Filichona.
                • Helichonidae Jankowski 1972. Heliochona.
                • Lobochonidae Jankowski 1967. Lobochona.
                • Phyllochonidae Jankowski 1972. Phyllochona.
                • Spirochonidae Stein 1854. Spirochona.
              • Cryptogemmida Jankowski 1975
                • Actinichonidae Jankowski 1973. Actinichona.
                • Echinichonidae Jankowski 1973. Echinichona.
                • Inversochonidae Jankowski 1973. Inversochona.
                • Isochonidae Jankowski 1973. Isochona.
                • Isochonopsidae Batisse & Crumeyrolle 1988. Isochonopsis.
                • Stylochonidae Mohr 1948. Stylochona.
        • Rhynchodia Chatton & Lwoff 1939
          • Hypocomidae Bütschli 1889. Hypocoma.
          • Rhynchodida Chatton & Lwoff 1939
            • Ancistrocomidae Chatton & Lwoff 1939. Ancistrocoma.
            • Sphenophryidae Chatton & Lwoff 1921. Sphenophrya.
        • Suctoria Claparède & Lachmann 1858
          • Exogenida Collin 1912
            • Allantosomatidae Jankowski 1967. Allantosoma.
            • Dentacinetidae Batisse 1992. Dentacineta.
            • Dendrosomididae Jankowski 1978. Dendrosomides.
            • Ephelotidae Kent 1882. Ephelota.
            • Lecanophryidae Jankowski 1973. Lecanophrya.
            • Manuelophryidae Dovgal 2002. Manuelophrya.
            • Metacinetidae Bütschli 1889. Metacineta.
            • Ophryodendridae Stein 1867. Ophryodendron.
            • Paracinetidae Jankowski 1978. Paracineta.
            • Phalacrocleptidae Kozloff 1966. Phalacrocleptes.
            • Podophryidae Haeckel 1866. Podophrya.
            • Praethecacinetidae Dovgal 1996. Praethecacineta.
            • Rhabdophryidae Jankowski 1970. Rhabdophrya.
            • Severonidae Jankowski 1981. Severonis.
            • Spelaeophryidae Jankowski in Batisse 1975. Spelaeophrya.
            • Tachyblastonidae Grell 1950. Tachyblaston.
            • Thecacinetidae Matthes 1956. Thecacineta.
          • Endogenida Collin 1912
            • Acinetidae Stein 1859. Acineta.
            • Acinetopsidae Jankowski 1978. Acinetopsis.
            • Choanophryidae Dovgal 2002. Choanophrya.
            • Corynophryidae Jankowski 1981. Corynophrya.
            • Dactylostomatidae Jankowski 1978. Dactylostoma.
            • Dendrosomatidae Fraipont 1878. Dendrosoma.
            • Endosphaeridae Jankowski in Corliss 1979. Endosphaera.
            • Erastophryidae Jankowski 1978. Erastophrya.
            • Pseudogemmidae Jankowski 1978. Pseudogemma.
            • Rhynchetidae Jankowski 1978. Rhyncheta.
            • Solenophryidae Jankowski 1981. Solenophrya.
            • Tokophryidae Jankowski in Small & Lynn 1985. Tokophrya.
            • Trichophryidae Fraipont 1878. Trichophrya.
          • Evaginogenida Jankowski in Corliss 1979
            • Cometodendridae Jankowski 1978. Cometodendron.
            • Cyathodiniidae da Cuhna 1914. Cyathodinium.
            • Dendrocometidae Haeckel 1866. Dendrocometes.
            • Discophryidae Collin 1912. Discophrya.
            • Enchelyomorphidae Augustin & Foissner 1992. Enchelyomorpha.
            • Heliophryidae Corliss 1979. Heliophrya.
            • Periacinetidae Jankowski 1978. Periacineta.
            • Prodiscophryidae Jankowski 1978. Prodiscophrya.
            • Rhynchophryidae Jankowski 1978. Rhynchophrya.
            • Stylocometidae Jankowski 1978. Stylocometes.
            • Trypanococcidae Dovgal 2002. Trypanococcus.
    • Colpodea Small & Lynn 1981
      • Bursariomorphida Fernández-Galiano 1978
        • Bryometopidae Jankowski 1980. Bryometopus (P), Thylakidium.
        • Bursaridiidae Foissner 1993. Bursaridium, Paracondylostoma.
        • Bursariidae Bory de St. Vincent 1826. Bursaria.
      • Colpodida de Puytorac et al. 1974. Incertae sedis taxa: Bardeliellidae Foissner 1984 (Bardeliella), Hausmanniellidae Foissner 1987 (Avestina, Hausmanniella), Ilsiellidae Bourland et al. 2011 (Ilsiella), Pseudochlamydonellidae Buitkamp et al. 1989 (Hackenbergia, Pseudochlamydonella) and Marynidae Poche 1913 (Maryna).
        • Bryophryina de Puytorac et al. 1979
          • Bryophryidae de Puytorac et al. 1979. Bryophrya.
          • Sandmanniellidae Foissner & Stoeck 2009. Sandmanniella.
        • Colpodina Foissner et al. 2011
          • Colpodidae Bory de St. Vincent 1826 (P). Colpoda.
          • Grandoriidae Corliss 1960. Grandoria.
          • Tillinidae Foissner et al. 2011. Tillina.
        • Grossglockneriidae Foissner 1980 [Grossglockneriina Foissner 1980]. Grossglockneria, Pseudoplatyophrya.
      • Cyrtolophosidida Foissner 1978
        • Cyrtolophosididae Stokes 1888. Cyrtolophosis.
        • Kreyellidae Foissner 1979. Kreyella.
      • Platyophryida de Puytorac et al. 1979
        • Ottowphryidae Foissner et al. 2011. Ottowphrya, Platyophryides.
        • Platyophryidae de Puytorac et al. 1979 (P). Platyophrya.
        • Sagittariidae Grandori & Grandori 1935. Sagittaria.
        • Sorogenidae Bradbury & Olive 1980. Sorogena.
        • Woodruffiidae Gelei 1954. Etoschophrya, Rostrophrya, Woodruffia.
    • Nassophorea (P)
      • Colpodidiidae Foissner 1995. Colpodidium.
      • Nassulida Jankowski 1967
        • Furgasoniidae Corliss 1979. Furgasonia, Wolfkosia.
        • Nassulidae de Fromentel 1874. Nassula, Obertrumia.
      • Microthoracida Jankowski 1967
        • Microthoracidae Wrzesniowski 1870. Drepanomonas, Microthorax.
        • Leptopharyngidae Kahl 1926. Leptopharynx, Pseudomicrothorax.
    • Prostomatea Schewiakoff 1896 (P)
      • Apsiktratidae Foissner et al. 1994 [Prostomatida Schewiakoff 1896]
        • Balanionidae Small & Lynn 1985. Balanion.
        • Cryptocaryonidae Wright & Colorni 2002. Cryptocaryon.
        • Colepidae Ehrenberg 1838. Coleps, Plagiopogon.
        • Holophryidae Perty 1852. Holophrya.
        • Lagynidae Sola et al. 1990. Lagynus.
        • Metacystidae Kahl 1926. Metacystis, Vasicola.
        • Placidae Small & Lynn 1985. Placus.
        • Plagiocampidae Kahl 1926. Plagiocampa.
        • Prorodontidae Kent 1881. Prorodon.
        • Urotrichidae Small & Lynn 1985. Urotricha.
    • Plagiopylea Small & Lynn 1985
      • Plagiopylida Small & Lynn 1985
        • Epalxellidae Corliss 1960. Epalxella, Saprodinium.
        • Plagiopylidae Schewiakoff 1896. Plagiopyla.
        • Sonderiidae Small & Lynn 1985. Sonderia.
        • Trimyemidae Kahl 1933. Trimyema.
    • Oligohymenophorea de Puytorac et al. 1974
      • Apostomatia Chatton & Lwoff 1928
        • Apostomatida Chatton & Lwoff 1928
          • Colliniidae Cépède 1910. Collinia, Metacollinia.
          • Cyrtocaryidae Corliss 1979. Cyrtocaryum.
          • Foettingeriidae Chatton 1911. Foettingeria.
          • Pseudocolliniidae Chantangsi et al. 2013. Fusiforma, Pseudocollinia.
        • Astomatophorida Jankowski 1966
          • Opalinopsidae Hartog 1906. Opalinopsis.
        • Pilisuctorida Jankowski 1966
          • Conidophryidae Kirby 1941. Conidophrys.
      • Astomatia Schewiakoff 1896
        • Anoplophryidae Cépède 1910. Anoplophrya.
        • Buetschliellidae de Puytorac in Corliss 1979. Buetschliella.
        • Clausilocolidae de Puytorac in Corliss 1979. Clausilocola.
        • Contophryidae de Puytorac 1972. Contophyra.
        • Haptophryidae Cépède 1923. Haptophrya.
        • Hoplitophryidae Cheissin 1930. Hoplitophrya.
        • Intoshellinidae Cépède 1910. Intoshellina.
        • Maupasellidae Cépède 1910. Maupasella.
        • Radiophryidae de Puytorac 1972. Radiophrya.
      • Hymenostomatia Delage & Hérouard 1896
        • Tetrahymenida Fauré-Fremiet in Corliss 1956. Incertae sedis taxa: Trichospiridae Kahl 1926 (Trichospira).
          • Curimostomatidae Jankowski 1968. Curimostoma.
          • Glaucomidae Corliss 1971. Glaucoma.
          • Spirozonidae Kahl 1926. Spirozona.
          • Tetrahymenidae Corliss 1952. Tetrahymena.
          • Turaniellidae Didier 1971. Colpidium, Dexiostoma, Turaniella.
        • Ophryoglenida Canella 1964
          • Ichthyophthiriidae Kent 1881. Ichthyophthirius.
          • Ophryoglenidae Kent 1881. Ophryoglena.
      • Peniculia Fauré-Fremiet in Corliss 1956 (P)
        • Peniculida Fauré-Fremiet in Corliss 1956
          • Clathrostomatidae Kahl 1926. Clathrostoma.
          • Frontoniidae Kahl 1926. Disematostoma, Frontonia (P).
          • Lembadionidae Jankowski in Corliss 1979. Lembadion.
          • Maritujidae Jankowski in Small & Lynn 1985. Marituja.
          • Neobursaridiidae Dragesco & Tuffrau 1967. Neobursaridium.
          • Parameciidae Dujardin 1840. Paramecium.
          • Paranassulidae Fauré-Fremiet 1962. Paranassula.
          • Stokesiidae Roque 1961. Stokesia.
        • Urocentridae Claparède & Lachmann 1858 [Urocentrida de Puytorac, Grain & Mignot 1987]
      • Peritrichia Stein 1859
        • Sessilida Kahl 1933
          • Astylozoidae Kahl 1935. Astylozoon, Hastatella.
          • Ellobiophryidae Chatton and Lwoff 1929. Ellobiophrya.
          • Epistylididae Kahl 1933. Epistylis.
          • Lagenophryidae Bütschli 1889. Lagenophrys.
          • Operculariidae Fauré-Fremiet in Corliss 1979. Opercularia.
          • Rovinjellidae Matthes 1972. Rovinjella.
          • Scyphidiidae Kahl 1933 (P). Scyphidia.
          • Termitophryidae Lom in Corliss 1979. Termitophrya.
          • Usconophryidae Clamp 1991. Usconophrys.
          • Vaginicolidae de Fromentel 1874. Cothurnia, Pyxicola, Thuricola, Vaginicola.
          • Vorticellidae Ehrenberg 1838. Carchesium, Epicarchesium (P), Ophrydium, Pelagovorticella, Pseudovorticella (P), Vorticella (P).
          • Zoothamniidae Sommer 1951. Haplocaulus, Zoothamnium.
        • Mobilida Kahl 1933
          • Polycyclidae Poljansky 1951. Polycycla.
          • Trichodinidae Claus 1874. Trichodina.
          • Trichodinopsidae Kent 1881. Trichodinopsis.
          • Urceolariidae Dujardin 1840. Leiotrocha, Urceolaria.
      • Scuticociliatia Small 1967 (P)
        • Philasterida Small 1967
          • Cohnilembidae Kahl 1933. Cohnilembus.
          • Cryptochilidae Berger in Corliss 1979. Cryptochilum.
          • Entodiscidae Jankowski 1973. Entodiscus.
          • Entorhipidiidae Madsen 1931. Entorhipidium.
          • Orchitophryidae Cépède 1910 (P). Orchitophrya.
          • Paralembidae Corliss & de Puytorac in Small & Lynn 1985. Anophrys, Paralembus.
          • Parauronematidae Small & Lynn 1985 (P). Parauronema (P).
          • Philasteridae Kahl 1931. Kahlilembus, Philaster.
          • Pseudocohnilembidae Evans & Thompson 1964. Pseudocohnilembus.
          • Schizocaryidae Jankowski 1979. Schizocaryum.
          • Thigmophryidae Chatton & Lwoff 1926. Thigmophrya.
          • Thyrophylacidae Berger in Corliss 1961. Thyrophylax.
          • Uronematidae Thompson 1964. Uronema.
          • Urozonidae Grolière 1975. Urozona.
        • Pleuronematida Fauré-Fremiet in Corliss 1956
          • Calyptotrichidae Small & Lynn 1985. Calyptotricha.
          • Conchophthiridae Kahl in Doflein and Reichenow 1929. Conchophthirus.
          • Ctedoctematidae Small & Lynn 1985. Ctedoctema.
          • Cyclidiidae Ehrenberg 1838 (P). Cristigera, Cyclidium.
          • Dragescoidae Jankowski 1980. Dragescoa.
          • Eurystomatellidae Miao et al. 2010. Eurystomatella.
          • Histiobalantiidae de Puytorac & Corliss in Corliss 1979. Histiobalantium.
          • Peniculistomatidae Fenchel 1965. Peniculistoma.
          • Pleuronematidae Kent 1881 (P). Pleuronema.
          • Thigmocomidae Kazubski 1958. Thigmocoma.
        • Thigmotrichida Chatton & Lwoff 1922
          • Ancistridae Issel 1903. Ancistrum.
          • Hemispeiridae König 1894. Hemispeira.
          • Hysterocinetidae Diesing 1866. Hysterocineta.
          • Paraptychostomidae Ngassam et al. 1994. Paraptychostomum.
        • Loxocephalida Jankowski 1964 (P)
          • Cinetochilidae Perty 1852 (P). Cinetochilum, Sathrophilus.
          • Loxocephalidae Jankowski 1964. Cardiostomatella, Dexiotricha, Loxocephalus.

Rhizaria Cavalier-Smith 2002

• Incertae sedis taxa: Gymnosphaerida Poche 1913, emend. Mikrjukov 2000. Actinocoryne, Cienkowskya, Gymnosphaera, Hedraiophrys [possible synonym of Cienkowskya], Wagnerella.

Cercozoa Cavalier-Smith 1998, emend. Adl et al. 2005; emend. Cavalier-Smith 2018

• Incertae sedis taxa:
  • Aquavolonida Bass & Berney 2018. Aquavolon, Lapot.^[124]
  • Tremulida Howe et al. 2011. Tremula.
  • Genera of uncertain placement: Dictiomyxa, Katabia, Myxodictyium, Pontomyxa, Protomyxa, Protogenes, Pseudospora, Rhizoplasma
  • Discocelia Cavalier-Smith 2013 [Discocelis Vørs 1988]
  • Psammonobiotidae* Golemansky 1974, emend. Meisterfeld 2002. Alepiella, Chardezia, Edaphonobiotus, Feuerbornia, Frenzelina, Lesquerella, Micramphora, Micropsammella, Nadinella, Ogdeniella, Psammonobiotus, Propsammonobiotus, Rhumbleriella.
• Sarcomonadea Cavalier-Smith 1993 emend. Cavalier-Smith 2018 (P)
  • Cercomonadida^[h] Poche 1913, emend. Vickerman 1983, emend. Mylnikov 1986, emend. Karpov et al. 2006; emend Howe et al. 2009; emend Cavalier-Smith 2012 [Cercomonadidae Kent 1880, emend. Mylnikov and Karpov 2004; Cercobodonidae Hollande 1942]. Cercomonas, Eoercomonas, Filomonas, Neocercomonas, Cavernomonas.
  • Paracercomonadida Cavalier-Smith 2018 [Paracercomonadidae Cavalier-Smith & Karpov 2012]. Brevimastigomonas, Metabolomonas, Nucleocercomonas, Paracercomonas, Phytocercomonas.
  • Glissomonadida Howe & Cavalier-Smith 2009 [Heteromitidae Kent 1880, emend. Mylnikov 1990, emend. Mylnikov & Karpov 2004]
    • Saccharomycomorphidae Feng, He, Jiang, Zhang & Yu 2021.^[125] Saccharomycomorpha.
    • Sandonidae Howe et al. 2009. Sandona, Flectomonas, Neoheteromita, Mollimonas.
    • Dujardinidae Howe & Cavalier-Smith 2011. Dujardina.
    • Bodomorphidae Hollande 1952, emend. Cavalier-Smith in Howe et al. 2009. Bodomorpha.
    • Proleptomonadidae Howe et al. 2009. Proleptomonas.
    • Allapsidae Howe & Cavalier-Smith 2009. Allapsa, Teretomonas, Allantion.
    • Viridiraptoridae Hess & Melkonian 2013. Orciraptor, Viridiraptor.
    • Pansomonadidae Vickerman in Vickerman et al. 2005. Agitata, Aurigamonas.
• Sainouroidea Schuler et al. 2018 [Helkesida Cavalier-Smith 2018]
  • Sainouridae Cavalier-Smith 2008. Acantholus, Cholamonas, Homocognata, Sainouron.
  • Helkesimastigidae Cavalier-Smith 2008. Helkesimastix.
  • Guttulinopsidae Olive 1970. Guttulinopsis, Olivorum, Puppisaman, Rosculus.
• Thecofilosea Cavalier-Smith 2003, emend. Cavalier-Smith 2011. Incertae sedis taxa: Mataza.
  • Phaeodarea Haeckel 1879 [Tripylea Hertwig 1879]
    • Phaeoconchia Haeckel 1879. Coelodendrum, Coelographis, Conchellium, Conchopsis.
    • Phaeocystina Haeckel 1879. Aulacantha, Aulographis, Cannoraphis.
    • Phaeogromia Haeckel 1879. Castanella, Challengeron, Haeckeliana, Medusetta, Tuscarora.
    • Phaeosphaeria Haeckel 1879. Aulosphaera, Cannosphaera, Sagosphaera.
  • Cryomonadida Cavalier-Smith 1993
    • Rhogostomidae Dumack et al. 2017. Rhogostoma, Sacciforma, Capsellina.
    • Protaspidae Cavalier-Smith 1993 [Cryomonadidae Cavalier-Smith 1993]. Cryothecomonas, Protaspa.
  • Ventricleftida Cavalier-Smith 2011
    • Ventrifissuridae Cavalier-Smith 2018. Ventrifissura.
    • Verrucomonadidae Cavalier-Smith 2018. Verrucomonas.
  • Tectofilosida Cavalier-Smith 2003
    • Chlamydophryidae De Saedeleer, 1934. Chlamydophrys Cienkowski 1876, Diaphoropodon Archer 1869, Lecythium Hertwig & Lesser 1874, Katarium Solbach 2024,^[126] Trachyrhizium Shiratori & Ishida 2016.
    • Psammonobiotidae Golemansky, 1974. Micropsamella.
    • ?Volutellidae Sudzuki, 1979. Pseudovolutella, Volutella.
    • Fiscullina Cavalier-Smith 2018
      • Fiscullidae Dumack, Mausbach and Bonkowski in Dumack et al. 2017. Fisculla, Omnivora.^[127]
      • Pseudodifflugiidae De Saedeleer 1934. Pseudodifflugia.
      • Rhizaspididae Skuja 1948. Rhizaspis.
  • Ebriacea Lemmermann 1901 [Ebriidae Poche 1913; Ebriida Deflandre 1936]. Ebria, Hermesinum, Botuliforma.
• Imbricatea Cavalier-Smith 2011
  • Spongomonadida Hibberd 1983 [Spongomonadidae Karpov 1990]. Rhipidodendron, Spongomonas.
  • Marimonadida Cavalier-Smith & Bass 2011
    • Abolliferidae Cavalier-Smith 2018. Abollifer, Cowlomonas, ?Heterochromonas.
    • Auranticordidae Cavalier-Smith 2018. Auranticordis, Rhabdamoeba.
    • Cyranomonadidae Cavalier-Smith 2018. Cyranomonas.
    • Pseudopirsoniidae Cavalier-Smith 2018. Pseudopirsonia.
  • Variglissida Cavalier-Smith 2014
    • Clautriaviidae Cavalier-Smith in Cavalier-Smith and Scoble, 2013. Clautriavia.
    • Nudifilidae Cavalier-Smith in Howe et al., 2011. Nudifila.
    • Quadriciliidae Cavalier-Smith 2018. Quadricilia.
  • Silicofilosea Adl et al. 2005, emend. Adl et al. 2012
    • Thaumatomonadida Shirkina 1987 [Thaumatomastigidae Patterson and Zoelfell 1991]
      • Thaumatomonadidae Hollande 1952. Allas, Hyaloselene, Reckertia, Thaumatomonas, Thaumatomastix, Ovaloplaca, Scutellomonas, Thaumatospina, Penardeugenia.
      • Peregriniidae Cavalier-Smith 2011. Gyromitus, Peregrinia.
      • Esquamulidae Shiratori, Yabuki & Ishida 2012. Esquamula.
    • Euglyphida Copeland 1956, emend. Cavalier-Smith 1997. Incertae sedis taxa: Phaeobola.^[128]
      • Cyphoderiidae de Saedeleer 1934. Campascus*, Corythionella, Cyphoderia [Schaudinnula], Messemvriella*, Pseudocorythion, Ichthyosquama, Knarr, Oleiformis, Psammoderia.^[129]
      • Paulinellidae de Saedeleer 1934, emend. Adl et al. 2012. Micropyxidiella, Ovulinata, Paulinella.
      • Euglyphina Kosakyan et al. 2016
        • Assulinidae Lara et al. 2007. Assulina, Placocista, Valkanovia*.
        • Sphenoderiidae Chatelain et al. 2013. Sphenoderia, Trachelocorythion, Deharvengia*.
        • Trinematidae Hoogenraad & De Groot 1940, emend Adl et al. 2012. Corythion, Playfairina*, Puytoracia*, Trinema.
        • Euglyphidae Wallich 1864, emend Lara et al. 2007. Euglypha, Scutiglypha.
        • Tracheleuglypha^[x] Deflandre 1928
    • Trivalvulariida Siemensma & Dumack 2020.^[130] Leptogromia, Trivalvularis.
• Metromonadea Cavalier-Smith 2007, emend. Cavalier-Smith 2011. Metromonas, Metopion, Micrometopion, Kiitoksia.
• Granofilosea Cavalier-Smith & Bass 2009.^[131] Incertae sedis taxa*: ?Apogromia, ?Kibisidytes, ?Leucodictyon, ?Limnofila, ?Mesofila, ?Microcometes, ?Microgromia, ?Nanofila, ?Reticulamoeba and probably ?Belaria, ?Ditrema, ?Heliomorpha [=Dimorpha] and ?Paralieberkuehnia.
  • Massisteridae Cavalier-Smith 1993. Massisteria, Minimassisteria.
  • Clathrulinidae Claus 1874 [Desmothoracida Hertwig and Lesser 1874]. Actinosphaeridium, Cienkowskya*, Clathrulina, Hedriocystis, Penardiophrys, ?Servetia.
• Chlorarachnea Hibberd & Norris 1984. Amorphochlora, Bigelowiella, Chlorarachnion, Cryptochlora, Gymnochlora, Lotharella, Minorisa, Partenskyella, Viridiuvalis.

Endomyxa Cavalier-Smith 2002, emend. Bass & Berney in Adl et al. 2019

• Vampyrellida West 1901, emend. Hess et al. 2012 [Aconchulinida De Saedeleer 1934]. Incertae sedis taxa: Arachnula, Gobiella, Lateromyxa, Penardia.^[132]
  • Thalassomyxa Grell 1985
  • Vampyrellidae Zopf 1885. Vampyrella.
  • Leptophryidae Hess, Sausen & Melkonian 2012. Arachnomyxa, Leptophrys, Planctomyxa, Platyreta, Pseudovampyrella,^[133] Theratromyxa, Vernalophrys.
  • Placopodidae Jahn 1928 [Hyalodiscidae Poche 1913]. Placopus.
  • Sericomyxidae More, Simpson & Hess 2021. Sericomyxa.
• Phytomyxea Engler & Prantl 1897
  • Marinomyxa Kolátková, Čepička, Hoffman & Vohník 2021^[134]
  • Plasmodiophorida Cook 1928 [Plasmodiophorales Engl. 1892;^[135] Plasmodiophoromycota R.H. Whittaker 1969^[1]]. Plasmodiophora [Ostenfeldiella], Polymyxa, Woronina, Ligniera [Anisomyxa; Rhizomyxa; Sorolpidium], Sorosphaerula [Tuburcinia; Sorosporium], Spongospora [Clathrosorus], ?Membranosorus, ?Octomyxa, ?Polymyxa, ?Sorodiscus, ?Tetramyxa [Molliardia; Thecaphora].^{[136][137][138]}
  • Phagomyxida Cavalier-Smith 1993. Phagomyxa, Maullinia.
• Filoreta Bass & Cavalier-Smith 2009
• Gromia Dujardin 1835
• Viscidocauda Shiratori & Ken-ichiro 2025^[139][140]
• Ascetosporea Sprague 1979, emend. Cavalier-Smith 2009
  • Haplosporida Caullery & Mesnil 1899. Bonamia, Haplosporidium, Minchinia, Urosporidium.
  • Mikrocytida Hartikainen et al. 2013. Mikrocytos, Paramikrocytos.
  • Paramyxida Chatton 1911. Marteilia, Paramyxa, Paramarteilia, Marteilioides, Eomarteilia.
  • Claustrosporidium Larsson 1987
  • Paradiniida Schiller 1935. Paradinium.

Retaria Cavalier-Smith 2002

• Foraminifera d'Orbigny 1826. Incertae sedis taxa: ?Lagenida, ?Heterogromia, ?Komokiacea*.
  • Monothalamids Pawlowski et al. 2013 (P) [currently under revision].^[141] All genera traditionally in Allogromiida, Astrorhizida, and the Xenophyophorea. Genera unplaced into families: Allogromia, Astrammina, Crithionina, Notodendrodes, Psammophaga, Bathysiphon.
    • Nujappikia Gooday & Holzmann 2022^[142]
    • Allogromiidae Rhumbler 1904. Vellaria.^[143]
    • Lieberkuehniidae Siemensma et al. 2021.^[144] Lieberkuehnia, Claparedellus.
    • Edaphoallogromiidae Siemensma et al. 2021.^[144] Edaphoallogromia.
    • Lacogromiidae Siemensma & Holzmann 2021.^[144] Lacogromia.
    • Limnogromiidae Holzmann & Siemensma 2021.^[144] Limnogromia.
    • Reticulomyxidae Page 1987, emend. Hülsmann 2014. Reticulomyxa, Dracomyxa, Haplomyxa,^[145] Wobo.
    • Schizamminidae Nørvang, 1961. Jullienella, Schizammina, Spiculosiphon.^[146]
    • Velamentofexidae Völcker & Clauß 2021.^[144] Velamentofex.
  • Tubothalamea Pawlowski et al. 2012. †Fusulinida Delage & Hérouard 1896 probably belongs to this group.^[3]
    • Miliolida Delage & Hérouard 1896. Alveolina, Cornuspira, Miliammina, Pyrgo, Quinqueloculina, Sorites.
    • Spirillinida Hohenegger & Piller 1975. Patellina, Spirillina.
    • Ammodiscidae Reuss 1862. Ammodiscus, Glomospira.
  • Globothalamea Pawlowski et al. 2012
    • Rotaliida Delage & Hérouard 1896
      • Planorbulinidae Schwager 1877. Planorbulinella, Hyalinea.
      • Discorboidea Ehrenberg 1838
        • Discorbidae Ehrenberg 1838. Discorbis.
        • Rosalinidae Reiss 1963. Rupertina, Discanomalina, "Rosalina", Gavelinopsis, Planorbulina.
      • Rotalioidea Ehrenberg 1839, emend. Pawlowski 2013. Incertae sedis taxa: ?Criboelphidium, ?"Elphidium", ?Protelphidium.
        • Elphidiidae Galloway 1933. Elphidium.
        • Ammoniidae Saidova 1981. Ammonia.
        • Elphidiellidae Holzmann & Pawlowski 2017. Elphidiella.
        • Haynesinidae Mikhalevich 2013. Haynesina, Aubignyna.
      • Glabratelloidea Loeblich & Tappan 1964
        • Rotaliellidae Loeblich & Tappan 1964. Rotaliella, Rossyatella.
        • Buliminoididae Seiglie 1970. Buliminoides.
        • Glabratellidae Loeblich & Tappan 1964. Glabratella, Glabratellina, Angulodiscorbis, Planoglabratella.
      • Calcarinoidea Schwager 1876
        • Calcarinidae Schwager 1876. Neorotalia, Baculogypsina, Baculogypsinoides, Schlumbergerella, Pararotalia.
      • Nummulitoidea de Blainville 1827
        • Nummulitidae de Blainville 1827. Nummulites, Operculinella, Cycloclypeus, Heterostegina, Operculina, Planoperculina, Planostegina.
      • Serioidea Holzmann & Pawlowski 2017
        • Uvigerinidae Haeckel 1894. Uvigerina, Rectuvigerina, Trifarina.
        • Bolivinitidae Glaessner 1937. Bolivina, Brizalina, Saidovina.
        • Cassidulinidae d'Orbigny 1839. Globocassidulina, Cassidulinoides, Evolvocassidulina, Islandiella, Ehrenbergina
        • Sphaeroidinidae Cushman 1927. Sphaeroidina.
        • Globobuliminidae Cushman 1927. Globobulimina.
      • Incertae sedis taxa:
        • ?Nonionidae Schultze 1854. Nonion, Nonionella, Nonionellina, Nonionoides.
        • ?Virgulinellidae Loeblich & Tappan 1984. Virgulinella.
        • ?Buliminidae Jones 1875. Bulimina.
        • ?Epistominellidae Holzmann & Pawlowski 2017. Epistominella.
        • ?Stainforthiidae Reiss 1963. Stainforthia, Gallitellia.
        • ?Cibicididae Cushman 1927. Cibicides, Cibicidoides, Heterolepa.
        • ?Chilostomellidae Brady 1881. Chilostomella.
        • ?Pullenidae Schwager 1877. Pullenia.
        • ?Nuttalidae Saidova 1981. Nuttalides.
        • ?Discorbinellidae Sigal 1952. Discorbinella, Hanzawaia.
        • ?Astrononionidae Cushman & Edwards 1937. Astrononion.
        • ?Oridorsalidae Loeblich & Tappan 1984. Oridorsalis.
        • ?Melonidae Holzmann & Pawlowski 2017. Melonis.
        • ?Cymbaloporidae Cushman 1927. Cymbaloporella.
        • ?Rubratelliidae Holzmann & Pawlowski 2017. Rubratella.
        • ?Murrayinelliidae Holzmann & Pawlowski 2017. Murrayinella.
    • Globigerinida Lankester 1885 emend. Arz, Arenillas & Gilabert 2022^[7] (P)
      • †Parvularugoglobigerinoidea Arenillas, Arz & Gilabert 2022
        • †Parvularuglobigerinidae Arenillas, Arz & Gilabert 2022. Pseudocaucasina, Palaeoglobigerina, Parvularugoglobigerina.
      • Eoglobigerinoidea BouDagher-Fadel 2012
        • †Eoglobigerinidae Blow 1979. Alicantina, Eoclavatorella, Eoglobigerina, Parasubbotina, Pseudoglobigerinella, Subbotina, Turbeogloborotalia.
        • Globoquadrinidae Blow 1979. Dentoglobigerina, Globoquadrina.
        • †Neoacarininidae BouDagher-Fadel 2012. Neoacarinina.
        • †Porticulasphaeridae Banner 1982. Globigerinatheka, Guembelitrioides, Inordinatosphaera, Orbulinoides, Porticulasphaera.
      • Globigerinoidea Carpenter, Parker & Jones 1862
        • Globigerinidae Carpenter, Parker & Jones 1862. Alloglobigerinoides, Ciperoella, Globigerina, Globicuniculus, Globigerinoides, Globigerinoidesella, Globoturborotalita, Trilobigerina [Trilobatus], Zeaglobigerina.
        • Globigerinellidae BouDagher-Fadel 2012. Beella, Bolliella, Globigerinella, Orcadia, Protentella, Quiltyella.
        • Hastigerinidae Bolli, Loeblich & Tappan 1957. Hastigerina, Hastigerinella, Hastigerinopsis.
        • Orbulinidae Schultze 1854. Biorbulina, Candorbulina, Orbulina, Praeorbulina.
        • Sphaeroidinellidae Banner & Blow 1959. Prosphaeroidinella, Sphaeroidinella, Sphaeroidinellopsis.
        • Turborotalitidae Hofker 1976. Berggrenia, Turborotalita.
      • Globorotalioidea Cushman 1927
        • †Catapsydracidae Bolli, Loeblich & Tappan 1957. Catapsydrax, Globigerinopsoides, Globigerinoita, Velapertina.
        • Globorotaloididae Banner & Blow 1959. Clavatorella, Globorotaloides, Protentelloides.
        • Globorotaliidae Cushman 1927. Dentigloborotalia, Globoconella, Globorotalia, Hirsutella, Jenkinsella, Menardella, Neogloboquadrina, Paragloborotalia, Truncorotalia.
        • Pulleniatinidae Cushman 1927. Pulleniatina.
      • †Globanomalinidoidea Loeblich & Tappan 1984
        • †Globanomalinidae Loeblich & Tappan 1984. Carinoturborotalia, Globanomalina, Luterbacheria, Planoglobanomalina, Turborotalia.
      • †Hantkeninoidea Cushman 1927
        • †Pseudohastigerinidae Canudo 1990. Pseudohastigerina.
        • †Hantkeninidae Cushman 1927. Applinella, Aragonella, Clavigerinella, Cribrohantkenina, Hantkenina.
      • †Truncorotaloidinoidea BouDagher-Fadel 2012
        • †Globigerapsidae Blow 1979. Globigerapsis, Muricoglobigerina.
        • †Planorotalitidae BouDagher-Fadel 2012. Astrorotalia, Planorotalites.
        • †Truncorotaloididae Loeblich & Tappan 1961. Acarinina, Igorina, Morozovella, Morozovelloides, Pearsonites, Praemurica, Pseudogloboquadrina, Testacarinata, Truncorotaloides.
    • †Globotruncanida Arz, Arenillas & Gilabert 2022^[7]
      • †Abathomphaloidea Arz, Arenillas & Gilabert 2022
        • †Abathomphalidae Pessagno 1967. Abathomphalus.
        • †Globotruncanellidae Maslakova 1964. Globotruncanella, Spinoglobotruncanella.
      • †Favuselloidea Longoria 1974
        • †Conoglobigerinidae BouDagher-Fadel, Banner & Whittaker 1997. Conoglobigerina, Tenuigerina, ?Sphaerogerina.
        • †Favusellidae Longoria 1974. Ascoliella, Favusella, Koutsoukosia.
        • †Globuligerinidae Loeblich & Tappan 1984. Compactogerina, Globuligerina, Haeuslerina, Petaloglobigerina.
      • †Hedbergelloidea Longoria & Gamper 1975
        • †Ananiidae El-Nakhal 2010. Anania, Badriella, Costellagerina, Hillsella, Liuenella [Liuella], Loeblichella, Muricohedbergella, Paracostellagerina, Pessagnoina, Planohedbergella, Pseudoclavihedbergella, Vanhintella.
        • †Hedbergellidae Loeblich & Tappan 1961. Asterohedbergella, Clavihedbergella, Hedbergella, Microhedbergella, Paraticinella, Pseudoguembelitria.
        • †Helvetoglobotruncanidae Lamolda 1976. Angulocarinella, Bermudeziana, Bollitruncana, Fingeria, Hedbergellita, Brittonella, Helvetoglobotruncana, Unitruncatus, Whiteinella.
        • †Praehedbergellidae Banner & Desai 1988. Blefuscuiana, Gorbachikella, Praehedbergella, Lilliputianella, Lilliputianelloides, Wondersella.
      • †Globotruncanoidea Brotzen 1942
        • †Globotruncanidae Brotzen 1942. Contusotruncana, Globotruncana, Marginotruncana, Obliquacarinata, Sphaerotruncana, Ventrotruncana.
        • †Praeglobotruncanidae Ion 1983. Concavatotruncana, Dicarinella, Falsotruncana, Rotundina, Praeglobotruncana, Verotruncana.
        • †Reissidae Korchagin 2001. Elevatotruncana, Globotruncanita, Kassabiana, Radotruncana, Sigalitruncana, Turbotruncana.
      • †Planomalinoidea Bolli, Loeblich & Tappan 1957
        • †Eohastigerinellidae Loeblich & Tappan 1984. Eohastigerinella, Hastigerinoides.
        • †Globigerinelloididae Longoria 1974. Alanlordella, Allotheca, Biglobigerinella, Blowiella, Claviblowiella, Globigerinelloides, Pseudoschackoina.
        • †Planomalinidae Bolli, Loeblich & Tappan 1957. Bannerina, Planomalina, Pseudoplanomalina.
        • †Schackoinidae Pokorný 1958. Asymetria, Groshenyia, Leupoldina, Neoschackoina, Schackoina.
      • †Rotaliporoidea Sigal 1958
        • †Rotaliporidae Sigal 1958. Anaticinella, Pseudothalmanninella, Rotalipora, Thalmanninella.
        • †Ticinellidae Longoria 1974. Biticinella, Claviticinella, Ticinella.
      • †Rugoglobigerinoidea Subbotina 1959
        • †Helvetiellidae Longoria & Gamper 1984. Archaeoglobigerina, Bucherina, Dorbignya, Edgarinella, Gandolfia, Gansserina, Globocarinata, Helvetiella, Kuglerina.
        • †Rugoglobigerinidae Subbotina 1959. Archaeoglobitruncana, Plummerita, Rugoglobigerina, Rugosocarinata, Rugotruncana, Trinitella.
    • †Heterohelicida Fursenko 1958, emend. Arz, Arenillas & Gilabert 2022^[7]
      • †Heterohelicoidea Cushman 1927
        • †Gublerinidae Aliyulla 1977. Gublerina, Lipsonia, Praegublerina.
        • †Heterohelicidae Cushman 1927. Braunella, Bronnimannella, Ehrenbergites, Globoheterohelix, Fleisherites, Hartella, Heterohelix, Huberella, Laeviheterohelix, Lazarusina, Lunatriella, Magellanina, Mihaia, Nederbragtina, Planoheterohelix, Protoheterohelix, Pseudoplanoglobulina, Steineckia, Striataella, Texasina, ?Bifarina, ?Rectoguembelina, ?Zeauvigerina.
        • †Pseudotextulariidae Maamouri & Salaj 1978. Planoglobulina, Pseudotextularia, Racemiguembelina.
        • †Pseudoguembelinidae Aliyulla 1977. Eicheriella, Leptobimodalia, Pseudoguembelina.
        • †Spiroplectidae Cushman 1911. Hendersonites [Hendersonia], Neohendersonites, Paraspiroplecta, Spiroplecta.
        • †Ventilabrellidae Maamouri & Salaj 1978. Planulitella, Proliferania, Sigalia, Ventilabrella.
    • †Guembelitriida Arenillas, Arz & Gilabert 2022^[7]
      • †Cassigerinelloidea Bolli, Loeblich & Tappan 1957
        • †Cassigerinellidae Bolli, Loeblich & Tappan 1957. Cassigerinella, Riveroinella.
      • †Guembelitrioidea Montanaro-Gallitelli 1957
        • †Guembelitriidae Montanaro-Gallitelli 1957. Cassigerinelloita, Guembelitria, Chiloguembelitria, Jenkinsina, ?Archaeoguembelitria, ?Gallitellia, ?Guembelitriella.
      • †Chiloguembelinoidea Reiss 1963
        • †Chiloguembelinidae Reiss 1963. Chiloguembelina, Woodringina, ?Streptochilus.
      • †Globoconusoidea BouDagher-Fadel 2012
        • †Globoconusidae BouDagher-Fadel 2012. Globoconusa, Trochoguembelitria,
    • Order ? (unnamed)^[7]
      • Globigerinitoidea BouDagher-Fadel 2012, emend. Arenillas, Arz & Gilabert 2022^[7]
        • Candeinidae Cushman 1927. Candeina.
        • †Globigerinatellidae BouDagher-Fadel 2012. Globigerinatella.
        • Globigerinitidae Bermúdez 1961. Globigerinita, Mutabella, Polyperibola, Tinophodella.
        • Tenuitellidae BouDagher-Fadel 2012. Praetenuitella, Tenuitella, Tenuitellinata, Tenuitellita.
        • †Family ? (unnamed). Dipsidripella, ?Antarcticella.
    • Robertinida Loeblich & Tappan 1984. Hoeglundina, Robertina, Robertinoides.
    • Textulariida Delage & Hérouard 1896 (P). Cyclammina, Eggerella, Reophax, Textularia, Trochammina.
    • Carterinida Loeblich & Tappan 1981. Carterina.
• Radiolaria Müller 1858, sensu Adl et al. 2005
  • Acantharea Haeckel 1881, emend. Mikrjukov 2000
    • Chaunocanthida Schewiakoff 1926. Amphiacon, Conacon, Gigartacon, Heteracon, Stauracon.
    • Holocanthida Schewiakoff 1926. Acanthochiasma, Acanthocolla, Acanthoplegma.
    • Symphyacanthida Schewiakoff 1926. Amphilithium, Astrolonche, Pseudolithium.
    • Arthracanthida Schewiakoff 1926. Acanthometra, Daurataspis, Dictyacantha, Diploconus, Phractopelta, Phyllostaurus, Pleuraspis, Stauracantha.
  • Taxopodida Fol 1883. Sticholonche.
  • Polycystinea Ehrenberg 1839 stat. nov. Levine et al. 1980^[147]
    • Spumellaria Ehrenberg 1876 stat. nov. Haeckel 1884
      • Hexacromyoidea Haeckel 1882 stat. nov. Suzuki et al. 2021 [Hexalonchata Afanasieva et al. 2005]
        • Hexacaryidae Haeckel 1882 stat. nov. Suzuki et al. 2021: Clevepilegma Dumatrica 2013, Haliphormis Ehrenberg 1846 [Hexastylanthus, Hexastylettus; Hexastylissus; Hexastylurus], Hexacaryum Haeckel 1882, Hexalonchetta Haeckel 1887, Hexancistra Haeckel 1879 [Hexancora], Hexapitys Haeckel 1882.
        • Hexacromyidae Haeckel 1882 stat. nov. Suzuki et al. 2021: ^?Carpocanthum Chen & Tan 1989, Hexacromyum Haeckel 1882 [Cubosphaera; Hexacontura], Hexalonchilla Haeckel 1887 [Hexalonchusa; Staurolonchantha], Nanina Kozur & Mostler 1982 [Pentactinosphaera].
        • Hollandosphaeridae Deflandre 1973: Anomalosoma Loeblich & Tappan 1961 [Heterosoma Hollande & Enjumet 1960, Hollandosphaera Deflandre 1973 [Heliaster Hollande & Enjumet 1960], Tetrapetalon Hollande & Enjumet 1960.
      • Spongosphaeroidea Haeckel 1862 → Spongosphaeridae Haeckel 1862: Diplospongus Mast 1910, Spongodendron Hollande & Enjumet 1960, Spongosphaera Ehrenberg 1847 [Hexadoridium; Spongosphaeromma].
      • Lithocyclioidea Ehrenberg 1846
        • Astracturidae Haeckel 1882: Astromma Ehrenberg 1846 [Astractinium; Astractura; Astracturium; Astrococcura; Staurococcura], Amphactura Haeckel 1882 [^?Dicoccura; ^?Diplactinium], Hymeniastrum Ehrenberg 1846 [Hymenastrella; Hymenactura; Hymenacturium; Trigonactinium; Hymenactinium; Pentactura; Trigonacturium].
        • Lithocycliidae Ehrenberg 1846: Cromyatractus Haeckel 1887 [Cromyatractium; Caryatractus], Heliosestrum Haeckel 1882 [Heliosestantha; Astrosestrum; Astrosestantha; Astrophacura; Staurodiscus Krasheninnikov 1960]; Heliostylus Haeckel 1882 [Astrostylus; Stylodiscus; Stylentodiscus], Lithocyclia Ehrenberg 1846 [Astrocyclia; Coccodiscus], Phacostaurus Haeckel 1882 [Phacostaurium, Astrostaurus, Crucidiscus, Heliostaurus, Sethostaurium, Sethostaurus, Staurentodiscus], Phacotriactis Sutton 1896, Sethostylus Haeckel 1882 [Sethostylium; Amphicyclia; Phacostylus; Phacostylium], Staurocyclia Haeckel 1882 [Coccostaurus], Triactiscus Haeckel 1882 [Trigonocyclia].
        • Panartidae Haeckel 1887: Cannartus Haeckel 1882 [Cannartidissa; Cannartiscus; Pipetta; Pipettaria; Pipettella; Druppula; Druppuletta], Diartus Sanfilippo & Riedel 1980, Didymocyrtis Haeckel 1862 [Artidium; Cyphinura; Cyphocolpus; Desmartus; Ommatocampula; Panaromium; Panartus; Panartella; Panartidium; Panartissa; Panartura; Peripanartium; Peripanartula; Peripanartus; Peripanicula], Spongolivella Dumitrica 2021.
        • Phacodiscidae Haeckel 1882: Periphaena Ehrenberg 1874 [Astrophacomma; Heliodiscomma; Perizona], Phacodiscus Haeckel 1882 [Phacodiscinus; Astrophacilla; Paracenodiscus; Phacodisculus; Prunulum; Prunuletta; Sethodiscinus].
      • Spongodiscoidea Haeckel 1862 emend. Suzuki 2021
        • Spongodiscidae Haeckel 1862: Spongaster Ehrenberg 1861 [Spongastrella; Histiastrella], Spongodiscus Ehrenberg 1854 [Spongodisculus], Spongotrochus Haeckel 1861 [Spongotrochiscus].
        • Euchitoniidae Stöhr 1880 emend. Suzuki 2021: Amphicraspedum Haeckel 1882 [Amphicraspedon; Aphirrhopella], Dictyocoryne Ehrenberg 1861 [Dictyocorynula; Dictyastrum; Dictyastrella; Euchitonia; ^?Hymenastromma; Rhopalodictya; Rhopalodictyum; Styla; Pteractis], Hexinastrum Haeckel 1882 [Hexalastromma; Pentalastromma; Pentinastrum], Ommatocampe Haeckel 1861 [Ommatocampium; Amphymenium], Tessarastrum Haeckel 1887 [Tessarastrella; Hagiastromma; Tessarostromma], Tricanastrum Haeckel 1879 [Dicranaster; Dicranastrum; Myelastrella; Myelastrum; Spongomyelastrum; Myelastromma; Pentophiastromma; Spongodicranastrum; Spongohagiastrum; Spongopentophiastrum; Spongostaurina; Tetracranastrum; Triastrum], Trigonastrum Haeckel 1887 [Trigonastrella; Rhopalastromma; Chitonastromma; Amphicraspedina; Amphirrhopoma; Dictyastromma; Monaxonium; Trigonastromma].
        • Spongobrachiidae Haeckel 1882 emend. Suzuki 2021: Spongasteriscus Haeckel 1862 [Spongasterisculus; Dictyocorynium], Spongastromma Haeckel 1887, Spongobrachium Haeckel 1882.
      • Cladococcoidea Haeckel 1862 stat. nov. Suzuki et al. 2021
        • Ethmosphaeridae Haeckel 1862: Cyrtidosphaera Haeckel 1861, Ethmosphaera Haeckel 1861, [Ethmosphaerella; Monosphaera], Haplosphaera Hollande & Enjumet 1960, Heliosphaera Haeckel 1861 [Heliosphaerella], Liosphaera Haeckel 1887 [Melitomma, Craspedomma].
        • Cladococcidae Haeckel 1862: Arachnosphaera Haeckel 1861 [Arachnosphaerella], Arachnospongus Mast 1910, Cladococcus Müller 1856 [Cladococcalis; Anomalacantha; Cladococcodes; Cladococcurus; Porococcus], Diplosphaera Haeckel 1861 [Diplosphaeromma; Astrosphaera; Diplosphaerella; Leptosphaera; Leptosphaerella; Astrosphaerella; Astrospongus; Drymosphaeromma; Leptosphaeromma], Haeckeliella Hollande & Enjumet 1960, Lychnosphaera Haeckel 1882 [Rhizoplegmidium, Rhizospongus, Thalassoplegma].
      • Trematodiscoidea Haeckel 1862 emend. Suzuki 2021 → Trematodiscidae Haeckel 1862 emend. Suzuki 2021: Flustrella Ehrenberg 1839 [Centrospira; Discospirella; Trematodiscus; Perichlamydium; Perispirella; Stylochlamyum], Staurospira Haeckel 1887 [Staurodictyon; Tholodiscus; Xiphospira], Stylodictya Ehrenberg 1846 [Stylodictyon; Stylochlamydium; Stylochlamys; Stylospongia; Stylocyclia; Stylospira], Tripodictya Haeckel 1882 [Xiphodictyon].
      • Haliommoidea Ehrenberg 1846
        • Actinommidae Haeckel 1862 emend. Suzuki 2021: Actinomma Haeckel 1861 [Actinommetta; Haliommura; ^?Rhaphidococcus; Riedelipyle; Dreyerella; Drymyomma; Cromyomma; Echinommura; Heliosomura; Spheropyle], Cromyechinus Haeckel 1882 [Cromyodrymus], Rhaphidocapsa Haeckel 1887, ^?Sphaeractis Brandt in Wetzel 1936, ^?Staurocaryum Haeckel 1882, Stomatosphaera Dreyer 1889, ^?Stuermeria Deflandre 1964.
        • Haliommidae Ehrenberg 1846 emend. Suzuki 2021: Cromyosphaera Haeckel 1882 [Cromyommetta; Cromyommura], Haliomma Ehrenberg 1839 [Actinommilla; Cenosphaera; Circosphaera; Thecosphaerella], Haliommantha Haeckel 1887, Hexacontella Haeckel 1887, Melittosphaera Haeckel 1882 [Conoactinomma], Pseudostaurosphaera Krasheninnikov 1960 [Pseudostaurolonche].
        • Heliodiscidae Haeckel 1882 sensu De Wever et al. 2001: Actinommura Haeckel 1887 [^?Excentrosphaerella], Excentrococcus Dumitrica 1978, Excentrodiscus Hollande & Enjumet 1960, Heliodiscus Haeckel 1862 [Heliodiscilla, Heliocladus, Heliodiscetta, Heliodrymus, Heliodendrum, Heliosestilla], Helioferrusa Dumitrica 2019, Phaenicosphaera Haeckel 1887 [Dreyeropyle].
      • Lithelioidea Haeckel 1862 sensu Matsuzaki et al. 2015
        • ^?†Conocaryommidae Lipman 1969: Conocaryomma Lipman 1969 [^?Conocromyomma].
        • Litheliidae Haeckel 1862 emend. Suzuki 2021: Lithelius Haeckel 1861 [Lithospira; ^?Azerbaidjanicus], Middourium Kozlova 1999 [Monobrachium], Spiremaria Kozlova 1960 [Spiromultitunica], Spongocyclia Haeckel 1862 [^?Lithocarpium; Ommatodiscinus; Ommatodiscus; Ommatodisculus].
        • †Phaseliformidae Pessagno 1972: Phaseliforma Pessagno 1972.
        • †Pyramispongiidae Kozur & Mostler 1978 sensu O'Dogherty 1994: Pyramispongia Pessagno 1973 [Nodotetraedra].
        • Sponguridae Haeckel 1862: Ommatogramma Ehrenberg 1861 [Spongurus; Spongocorisca; ^?Spongurantha; Spongurella].
      • Spongopyloidea Dreyer 1889 emend. Suzuki 2021
        • Spongopylidae Dreyer 1889 emend. Suzuki 2021: Schizodiscus Dogiel in Dogiel & Reshetnyak 1952, Spongobrachiopyle Kozur & Mostler 1978, Spongopyle Dreyer 1889 [Spongopylarium], Spongospira Stöhr 1880.
        • Cristallosphaeridae Popofsky 1912: Calcaromma Thomson 1877 [Cristallosphaera], Enalomelon Sugiyama 1992.
        • ^?Prunopylidae Poche 1913: Prunopyle Dreyer 1889, Spongopylidium Dreyer 1889.
      • Phorticioidea Haeckel 1882 stat. nov. Suzuki et al. 2021 [Larnacillilae De Wever et al. 2001]
        • Amphitholidae Haeckel 1887 stat. nov. sensu De Wever et al. 2001
        • Circodiscidae Dumitrica 1989 stat. nov. Suzuki et al. 2021
        • Cryptolarnaciidae Dumitrica 1989 stat. nov. Suzuki et al. 2021
        • Histiastridae Dumitrica 1989 stat. nov. Suzuki et al. 2021
        • Phorticiidae Haeckel 1882 sensu Dumitrica 1989
      • Larcospiroidea Haeckel 1887 stat. nov. sensu Dumitrica 1989
        • Dipylissidae Dumitrica 1989 stat. nov. Suzuki et al. 2021
        • Larcospiridae Haeckel 1887 stat. nov. Suzuki et al. 2021
        • Palaeotetrapylidae Dumitrica 1989 stat. nov. Suzuki et al. 2021
        • Pylodiscidae Haeckel 1887 sensu Dumitrica 1989
        • Zonariidae Haeckel 1887 sensu Dumitrica 1989
      • Pseudoaulophacoidea Riedel 1967 sensu De Wever et al. 2001
        • Patulibracchiidae Pessagno 1971 sensu De Wever et al. 2001
        • Pseudoaulophacidae Riedel 1967 sensu De Wever et al. 2001
        • Suttoniidae Schaaf 1976 sensu Dumitrica 2019
      • Stylosphaeroidea Haeckel 1887 sensu Dumitrica 1984
        • Entapiidae Dumitrica in De Wever, Dumitrica, Caulet Nigrini & Caridroit 2001
        • Stylatractidae Schröder 1909 emend. Suzuki 2021
        • Tubosphaeridae Suzuki 2021
    • Nassellaria Ehrenberg 1875 emend. Haeckel 1887. Artostrobus, Eucyrtidium, Lithomelissa, Pterocanium, Pterocorys.
    • Collodaria Haeckel 1887. Acrosphaera, Collosphaera, Collozoum, Sphaerozoum, Rhaphidozoum, Siphonsphaera, Thalassicolla.
    • Orodaria Nakamura & Suzuki 2020^[148]
      • Oroscenidae Haeckel 1887 emend. Nakamura & Suzuki 2021 [Orosphaerida Haeckel 1887; Orosphaeridae Haecker 1908]. Oroscena, Orostaurus, Oropelex. Nomina dubia genera: Orosphaera, Orodictyum, Orona, Oronium.
      • Thalassothamnidae Haecker 1906 emend. Nakamura & Suzuki 2021 [Cytocladidae Schröder, 1908]. Thalassothamnus, Cytocladus. Nomen dubium genus: Conostylus.
    • †Entactinaria Kozur & Mostler 1982 sensu Nakamura & Suzuki 2020^[y]
      • †Entactiniidae Riedel 1967. Afanasievella, Apophysiactinia, Borisella, Callela, Cancellosphaera, Costaentactinia, Cyclocarpus nomen dubium, Duodecimentactinia, Langsonsphaera,^[149] Entactinosphaera, Gracilentactinia, Holdisphaera, Involutentactinia, Kashiwara, Magnentactinia, Magnisphaera, Microporosa, Moskovistella, Multientactinia, Munzuwonella, Paratriposphaera, Perforentactinia, Plenoentactinia, Plenosphaera, Pluristratoentactinia, Polyedroentactinia, Provisocyntra, Radiobisphaera, Retentactinia, Retisphaera, Sinosphaera, Spongentactinia, Stigmosphaerostylus, Trilonche, Uberinterna, Wuyia.^[150]
      • †Tetrentactiniidae Kozur & Mostler 1979. Multisphaera.
      • †Triassothamnidae Takahashi, Maekawa & Dumitrica 2022. Triassothamnus.^[149]

Haptista Cavalier-Smith 2003

• Haptophyta Hibberd 1976, ex. Edvardsen & Eikrem 2000
  • Pavlovales Green 1976 [Pavlovophyceae Cavalier-Smith 1986]. Diacronema, Exanthemachrysis, Pavlova, Rebecca.
  • Prymnesiophyceae Hibberd 1976
    • Prymnesiales Papenfuss 1955, emend. Edvardsen & Eikrem 2000. Chrysochromulina, Chrysocampanula, Dicrateria, Haptolina, Prymnesium, Pseudohaptolina.
    • Phaeocystales Medlin 2000. Phaeocystis.
    • Isochrysidales Pascher 1910, emend. Edvardsen & Eikrem 2000. Emiliania, Gephyrocapsa, Isochrysis, Ruttnera, Tisochrysis.
    • Coccolithales Schwarz 1932, emend. Edvardsen & Eikrem 2000. Balaniger, Calciosolenia, Coccolithus, Hymenomonas, Chrysotila, Wigwamma.
  • Rappephyceae M. Kawachi, R. Kamikawa & T. Nakayama 2021^[151]
    • Pavlomulinales M. Kawachi & I. Inouye 2021. Pavlomulina.
• Centroplasthelida Febvre-Chevalier & Febvre 1984 [Centrohelea Kühn 1926 sensu Cavalier-Smith in Yabuki et al. 2012; Centroheliozoa Dürrschmidt & Patterson 1987]
  • ?Parasphaerastrum.
  • ?Spiculophryidae Shɨshkin & Zlatogursky 2018. Spiculophrys.
  • Pterocystida Cavalier-Smith and von der Heyden 2007, emend. Shɨshkin and Zlatogursky 2018
    • Raphidista Shɨshkin & Zlatogursky 2018
      • Choanocystidae Cavalier-Smith & von der Heyden 2007. Choanocystis.
      • Raphidiophryidae Febvre-Chevalier & Febvre 1984, emend. Shɨshkin & Zlatogursky 2018. Raphidiophrys.
    • Pterista Shɨshkin & Zlatogursky 2018
      • Oxnerellidae Cavalier-Smith & Chao 2012. Oxnerella.
      • Pterocystidae Cavalier-Smith & von der Heyden 2007. Pterocystis, Raineriophrys, Chlamydaster, Pseudoraphidiophrys, Pseudoraphidocystis, Triangulopteris,^[152] Khitsovia.^[153]
      • Heterophryidae Poche 1913, emend. Cavalier-Smith & von der Heyden 2007. Heterophrys, Sphaerastrum.
  • Panacanthocystida Shɨshkin & Zlatogursky 2018
    • Yogsothothidae Shɨshkin & Zlatogursky 2018 [Chthonida Shɨshkin & Zlatogursky 2018; Yogsothothina Shɨshkin & Zlatogursky 2018]. Yogsothoth.
    • Acanthocystida Cavalier-Smith & von der Heyden 2007 emend. Shɨshkin & Zlatogursky 2018
      • Marophryidae Cavalier-Smith & von der Heyden 2007 emend. Shɨshkin & Zlatogursky 2018 [Marophryina Cavalier-Smith in Yabuki et al. 2012]. Marophrys.
      • Chalarothoracina Hertwig & Lesser 1874 sensu Cavalier-Smith in Yabuki et al. 2012 emend. Shɨshkin & Zlatogursky 2018
        • Acanthocystidae Claus 1874 emend. Shɨshkin & Zlatogursky 2018. Acanthocystis.
        • Raphidocystidae Zlatogursky 2018. Raphidocystis.

Cryptista Cavalier-Smith 1989, 2018, emend. Adl et al. 2019

• Palpitia Cavalier-Smith & Chao 2012 → Palpitea Cavalier-Smith & Chao 2012 → Palpitida Cavalier-Smith & Chao 2012 → Palpitidae Cavalier-Smith & Chao 2012. Palpitomonas Yabuki & Ishida 2010.
• Rollomonadia Cavalier-Smith 2013 [Cryptophyta Silva 1962; Cryptophyta Cavalier-Smith 1986]
  • Kathablepharida^ICZN/Katablepharidophyta^ICN Okamoto & Inouye 2005 → Kathablepharidea^ICZN/Katablepharidophyceae^ICN Okamoto & Inouye 2005 [Leucocryptea Cavalier-Smith 2004] → Kathablepharidida^ICZN/Katablepharidales^ICN Okamoto & Inouye 2005 → Kathablepharididae^ICZN Vørs 1992 emend. Clay & Kugrens 1999/Kathablepharidaceae^ICN Skuja 1939.^[8] Hatena Okamoto & Inouye 2006, Kathablepharis Skuja 1939, Leucocryptos Butcher 1967, Platychilomonas Larsen & Patterson 1990, Roombia Okamoto, Chantangsi, Horák, Leander & Keeling 2009.
  • Cryptomonada Cavalier-Smith 2004
    • Cyathomonadacea Pringsheim 1944
      • Goniomonadidae Hill 1991. Goniomonas [previously Cyathomonas].
      • Hemiarmidae Cavalier-Smith 2017. Hemiarma.^[74]
    • Cryptophyceae Fritsch in West & Fritsch 1927 [Cryptomonadea Stein 1878 emend. Schoenichen 1925]. Incertae sedis taxa: Bjornbergiella Bicudo 1965,^[154] Cyanomonas, Plagioselmis.^[155]
      • Cryptomonadales Pascher 1913 emend. Clay et al. 1999
        • Baffinellaceae Daugbjerg & Norlin 2018. Baffinella.^[156]
        • Cryptomonadaceae Clay et al. 1999. Cryptomonas, Chilomonas.
      • Pyrenomonadales Clay et al. 1999
        • Pyrenomonadaceae Novarino & Lucas 1993. Pyrenomonas [=Rhodomonas], Storeatula, Rhinomonas.
        • Geminigeraceae Clay et al. 1999. Geminigera, Teleaulax, Hanusia, Guillardia, Proteomonas.
        • Chroomonadaceae Clay et al. 1999. Chroomonas, Falcomonas, Komma.
        • Hemiselmidaceae Butcher 1967. Hemiselmis.
      • ?Tetragonidiales Kristiansen 1992. Tetragonidium.^[z]

Excavates

Malawimonadida Cavalier-Smith 2003

• Malawimonadidae O' Kelly & Nerad 1999. Gefionella, Malawimonas.
• Imasidae Heiss, Simpson, & Kim 2020. Imasa.^[158]

Metamonada Grassé 1952, emend. Cavalier-Smith 1987

• Barthelona Bernard, Simpson & Patterson 2000^[159]
• Skoliomonas Eglit & Simpson 2024^[160]
• Anaeramoebae^[161] [Anaeramoebidae Táborský, Pánek & Čepička 2017]. Anaeramoeba.^[162]
• Fornicata Simpson 2003
  • "Carpediemonas-like organisms" (Kolisko et al. 2010) (P). Aduncisulcus, Carpediemonas, Dysnectes, Ergobibamus, Hicanonectes, Kipferlia.
  • Diplomonadida Wenyon 1926
    • Hexamitinae Kent 1880. Enteromonas, Gyromonas*, Hexamita, Spironucleus, Trepomonas, Trigonomonas*, Trimitus.
    • Giardiinae Kulda & Nohýnková 1978. Brugerolleia*, Giardia, Octomitus.
  • Retortamonadida Grassé 1952 (P). Chilomastix, Retortamonas.
  • Caviomonadidae Cavalier-Smith 2013. Caviomonas*, Iotanema.
• Parabasalia Honigberg 1973
  • ?Tricercomitus
  • Trichomonadida Kirby 1947. Cochlosoma, Dientamoeba, Lacusteria, Pentatrichomonas, Pentatrichomonoides, Pseudotrichomonas, Pseudotrypanosoma, Tetratrichomonas, Trichomonas, Trichomonoides, Trichomitopsis.
  • Honigbergiellida Čepička et al. 2010 (P?). Ditrichomonas, Cthulhu, Cthylla, Hexamastix, Honigbergiella, Monotrichomonas.
  • Hypotrichomonadida Čepička et al. 2010. Hypotrichomonas, Trichomitus.
  • Tritrichomonadida Čepička et al. 2010 (P?). Dientamoeba, Histomonas, Monocercomonas, Parahistomonas, Simplicimonas, Tritrichomonas.
  • Cristamonadida Brugerolle & Patterson 2001. Caduceia, Calonympha, Coronympha, Deltotrichonympha, Devescovina, Foaina, Gigantomonas, Joenia, Joenina, Joenoides, Joenopsis*, Kofoidia, Koruga, Macrotrichomonas, Macrotrichomonoides, Metadevescovina, Mixotricha, Pachyjoenia*, Projoenia*, Pseudodevescovina, Rhizonympha*, Snyderella, Stephanonympha.
  • Spirotrichonymphida Grassé 1952. Holomastigotes*, Holomastigotoides, Microjoenia*, Micromastigotes*, Rostronympha*, Spiromastigotes*, Spironympha*, Spirotrichonympha*, Spirotrichonymphella, Uteronympha*.
  • Lophomonadida Light 1927. Lophomonas.
  • Trichonymphida Poche 1913. Barbulanympha, Eucomonympha, Heliconympha, Hoplonympha, Leptospironympha, Macrospironympha*, Pseudotrichonympha, Rhynchonympha*, Spirotrichosoma*, Staurojoenina, Teranympha, Trichonympha, Urinympha.
• Preaxostyla Simpson 2003
  • Oxymonadida Grassé 1952. Barroella, Blattamonas, Brachymonas, Dinenympha, Microrhopalodina, Monocercomonoides, Notila, Opisthomitus, Oxymonas, Paranotila, Polymastix, Pyrsonympha, Sauromonas, Saccinobaculus, Streblomastix, Tubulimonoides.
  • Trimastigidae Saville Kent 1880-1882. Trimastix.
  • Paratrimastigidae Zhang et al. 2015. Paratrimastix.

Discoba Simpson in Hampl et al. 2009

Jakobida Cavalier-Smith 1993

• Ophirinina Yabuki, Gyaltshen, Heiss & Kim 2018^[163]
  • Agogonidae Galindo, Prokina, Torruella, López-García & Moreira 2023. Agogonia.^[164]
  • Ophirinidae Yabuki, Gyaltshen, Heiss & Kim 2018. Ophirina.
• Andalucina Cavalier-Smith 2013
  • Andaluciidae Cavalier-Smith 2013. Andalucia.
  • Stygiellidae Pánek, Táborský & Čepička 2015.^[165] Stygiella, Velundella.
• Histionina Cavalier-Smith 2013. Histiona, Jakoba, Moramonas, Reclinomonas, Seculamonas nomen nudum.

Tsukubamonadida Yabuki et al. 2011

• Tsukubamonadidae Yabuki et al. 2011. Tsukubamonas.

Heterolobosea Page & Blanton 1985

• Pharyngomonada Cavalier-Smith 2008. Pharyngomonas
• Tetramitia Cavalier-Smith 1993
  • Selenaionidae Hanousková et al. 2018. Dactylomonas, Selenaion.
  • Neovahlkampfiidae Hanousková et al. 2018. Neovahlkampfia.
  • Eutetramitia Hanousková et al. 2018
    • Vahlkampfiidae Jollos 1917 (P). Fumarolamoeba, Heteramoeba, Naegleria, Neovahlkampfia, Paravahlkampfia, Tetramitus, Vahlkampfia, Willaertia.
    • Gruberellidae Page & Blanton 1985. Gruberella*, Stachyamoeba.
    • Acrasidae Poche 1913. Acrasis, Allovahlkampfia, Pocheina.
    • Percolomonadidae Cavalier-Smith 2008. Percolomonas.
    • Psalteriomonadidae Cavalier-Smith 1993. Harpagon, Psalteriomonas, Monopylocystis, Pseudoharpagon, Sawyeria.
    • Stephanopogonidae Corliss 1961. Stephanopogon.
  • Creneidae Pánek et al. 2014. Creneis.
  • Tulamoebidae Kirby et al. 2015. Pleurostomum, Tulamoeba.

Euglenozoa Cavalier-Smith 1981, emend. Simpson 1997

• Euglenida Butschli 1884, emend. Simpson 1997. Uncertain genera: †Moyeria Thusu 1973.^[166]
  • Petalomonadida Cavalier-Smith 1993. Atraktomonas*, Biundula*, Calycimonas, Dolium, Dylakosoma*, Notosolenus, Pentamonas*, Petalomonas, Scytomonas, Sphenomonas, Tropidoscyphus*.^[167]
  • Alistosa Lax & Simpson 2021. Ploeotia, Serpenomonas, Keelungia, Lentomonas, Decastava.^[168]
  • Entosiphon Cavalier-Smith, Chao & Vickerman 2016^[169][170]
  • Gaulosia Lax, Cho & Keeling 2023^[170]
  • Karavia Lax, Cho & Keeling 2023. Hemiolia, Liburna.^[170]
  • Olkaspira Lax & Simpson 2021.^[168]
    • Chelandium Lax, Cho & Keeling 2023^[170]
    • Olkasia Lax, Lee, Eglit & Simpson 2019^[171]
    • Spirocuta Cavalier-Smith, Chao & Vickerman 2016^[169] [Helicales Perschke et al. 2017]^[168]
      • Anisonemia Cavalier-Smith 2016
        • Anisonemidae Kent 1880 emend. Cavalier-Smith 2016. Anisonema, Dinema (P), Heteronema.
        • Natomonadida Cavalier-Smith 2016
          • Neometanemidae Cavalier-Smith 2016. Neometanema.
          • Aphagea Cavalier-Smith 1993 emend. Busse & Preisfeld 2003 [Rhabdomonadina Leedale 1967 emend. Cavalier-Smith 1993].^[172] Astasia, Distigma, Gyropaigne, Menoidium, Parmidium, Rhabdomonas.^[168]
      • Peranemidae Bütschli 1884 (P). Chasmostoma, Jenningsia [Peranemopsis],^[173] Peranema, Teloprocta, Urceolus [Urceolopsis, Phialonema].^{[174][172][168][175]}
      • Euglenophyceae Schoenichen 1925, emend. Marin & Melkonian 2003 [Euglenea Butschli 1884, emend. Busse & Preisfeld 2002]
        • Rapaza Yamaguchi et al. 2012
        • Eutreptiales Leedale 1967, emend. Marin & Melkonian 2003. Eutreptia, Eutreptiella.
        • Euglenales Leedale 1967, emend. Marin & Melkonian 2003
          • Phacaceae Kim et al. 2010. Discoplastis, Lepocinclis, Phacus.
          • Euglenaceae Dujardin 1841, emend. Kim et al. 2010. Ascoglena, Colacium, Cryptoglena, Euglena, Euglenaformis, Euglenamorpha, Euglenaria, Euglenopsis, Hegneria, Klebsina, Monomorphina, Strombomonas, Trachelomonas.
• Diplonemea Cavalier-Smith 1993, emend. Simpson 1997
  • Diplonemidae Cavalier-Smith 1993, emend. Adl et al. 2019. Diplonema, Rhynchopus, Lacrimia, Sulcionema, Flectonema.
  • Hemistasiidae Cavalier-Smith 2016, emend. Adl et al. 2019. Hemistasia.
  • Eupelagonemidae Okamoto & Keeling 2018. Eupelagonema.
• Symbiontida Yubuki et al. 2009. Bihospites, Calkinsia, Postgaardi.
• Kinetoplastea Honigberg 1963. Incertae sedis taxa: ?Bordnamonas, ?Cephalothamnium, ?Rhynchoidomonas.
  • Prokinetoplastina Vickerman in Moreira et al. 2004. Ichthyobodo, Perkinsela.
  • Metakinetoplastina Vickerman in Moreira et al. 2004
    • Family Allobodonidae Goodwin, Lee, Kugrens & Simpson 2018.^[176] Genera: Allobodo Goodwin, Lee, Kugrens & Simpson 2018; Novijibodo Packer, Weston, Eglit & Simpson 2025.^[177]
    • Neobodonida Vickerman in Moreira et al. 2004. Actuariola, Avlakibodo,^[178] Azumiobodo, Cruzella, Cryptaulaxella,^[179] Dimastigella, Klosteria, Neobodo, Phanerobia, Rhynchobodo, Rhynchomonas.
    • Parabodonida Vickerman in Moreira et al. 2004. Cryptobia, Jarrellia, Parabodo, Procryptobia, Trypanoplasma.
    • Eubodonida Vickerman in Moreira et al. 2004. Bodo.
    • Trypanosomatida Kent 1880, emend. Vickerman in Moreira et al. 2004 → Trypanosomatidae Dolfein 1901. Angomonas, Blechomonas, Leptomonas, Paratrypanosoma, Sergeia, Strigomonas, Wallaceina, Phytomonas, Trypanosoma, †Paleoleishmania G.Poinar & R.Poinar 2004.^[180]
      • Leishmaniinae Maslov & Lukeš 2012. Borovskyia, Crithidia, Leptomonas, Lotmaria, Novymonas, Porcisia, Zelonia, Endotrypanum, Leishmania.

Orphan groups

• Meteora sporadica Hausmann, Weitere, Wolf & Arndt, 2002^[181]

Ancyromonadida Cavalier-Smith 1998

• Divimonas Barkhouse, Eglit, Weston & Simpson 2025^[182]
• Ancyromonadidae Cavalier-Smith 2008. Ancyromonas, Nutomonas.
• Planomonadidae Cavalier-Smith 1993. Fabomonas, Planomonas.

CRuMs Brown et al. 2018

• Diphyllatea Cavalier-Smith 2003 → Diphylleida Cavalier-Smith 1993 [Anisomonadea Cavalier-Smith 1993 emend. 2000] → Collodictyonidae Brugerolle et al. 2002, emend. Adl et al. 2019 [Diphylleidae Cavalier-Smith 1993; Sulcomonadidae Cavalier-Smith 2013]: Collodictyon Carter 1865, Diphylleia Massart 1920 [Aulacomonas Skuja 1939], Sulcomonas Brugerolle 2006.
• Hilomonadea Cavalier-Smith 2008 emend. 2012 → Rigifilida Cavalier-Smith in Yabuki et al. 2012 [Micronucleariida Cavalier-Smith 2008]
  • Micronucleariidae Cavalier-Smith 2008: Micronuclearia Mikrjukov & Mylnikov 2001.
  • Rigifilidae Yabuki & Cavalier-Smith in Yabuki et al. 2012: Rigifila Yabuki & Cavalier-Smith 2012.
• Glissodiscea Cavalier-Smith 2013 emend. 2021 → Mantamonadida Cavalier-Smith in Glücksman et al. 2011 → Mantamonadidae Cavalier-Smith in Glücksman et al. 2011: Mantamonas Glücksman & Cavalier-Smith 2011.
• (Glissandrida Yazaki et al. 2025 → Glissandridae Yazaki et al. 2025):^[183] Glissandra Patterson and Simpson 1996^[184]

Hemimastigophora Foissner et al. 1988

• Spironematellidae Silva 1980 emend. Shɨshkin 2022 [Spironemidae Doflein 1916 nom. inval.]. Hemimastix Foissner, Blatterer & Foissner 1988, Spironematella Silva 1970 emend. Shɨshkin 2022 [Spironema Klebs 1893 nom. inval.], Stereonema Foissner & Foissner 1993.^[185]
• Paramastigidae Skuja 1948 emend. Karpov 2012. Paramastix Skuja 1948.^[185]

Provora Tikhonenkov et al. 2022

• Nibbleridia Tikhonenkov et al. 2022 → Nibbleridea Tikhonenkov et al. 2022 → Nibbleridida Tikhonenkov et al. 2022 → Nibbleridae Tikhonenkov et al. 2022: Nibbleromonas Tikhonenkov et al. 2022, Ubysseya Tikhonenkov et al. 2022.^[12]
• Nebulidia Tikhonenkov et al. 2022 → Nebulidea Tikhonenkov et al. 2022 → Nebulidida Tikhonenkov et al. 2022 → Nebulidae Tikhonenkov et al. 2022: Nebulomonas Tikhonenkov et al. 2022, Ancoracysta Janouškovec, Tikhonenkov, Burki, Howe, Rohwer, Mylnikov & Keeling 2017.^[12]

Genera of uncertain affiliation

Acinetactis, Actinastrum, Actinocoma, Actinolophus, Adinomonas, Aletium, Amphimonas, Amylophagus, Aphelidiopsis, Asterocaelum, Asthmatos, Aurospora, Barbetia, Berkeleyaesol,^[186] Belaria, Belonocystis, Bertarellia, Bertramia, Bodopsis, Boekelovia, Branchipocola, Camptoptyche, Chalarodora, Cibdelia, Cichkovia, Cinetidomyxa, Cingula, Cladomonas, Clathrella, Codonoeca, Coelosporidium^[aa], Copromonas, Cyanomastix, Cyclomonas, Cytamoeba, Dallingeria, Dictyomyxa, Dimastigamoeba, Dinemula, Dinoasteromonas, Diplocalium, Diplomita, Diplophysalis, Diploselmis, Dobellina, Ducelleria, Ectobiella, Elaeorhanis, Embryocola, Endamoeba, Endemosarca, Endobiella, Endomonas, Endospora, Enteromyxa, Eperythrocytozoon, Errera, Fromentella, Gweamonas,^[187] Gymnococcus, Gymnophrydium, Haematotractidium, Hartmannina, Heliobodo, Heliomonas, Hermisenella, Heterogromia, Hillea, Hyalodaktylethra, Immanoplasma, Isoselmis, Janickina, Kamera, Labyrinthomyxa Dubosq 1921,^[ab] Lagenidiopsis, Liegeosia, Luffisphaera^[ac], Lymphocytozoon, Lymphosporidium, Macappella, Magosphaera, Malpighiella, Martineziella, Megamoebomyxa, Meringosphaera, Microcometes, Monochrysis, Monodus, Mononema, Myrmicisporidium, Naupliicola, Nephrodinium, Neurosporidium, Orbulinella, Ovicola, Palisporomonas, Pansporella, Paradinemula, Parakaryon^[ad], Paraluffisphaera, Paramonas, Paraplasma, Parastasia, Parastasiella, Peliainia, Peltomonas, Petasaria, Phagodinium, Phanerobia, Phloxamoeba, Phyllomitus, Phyllomonas, Physcosporidium, Pleuophrys, Pleuromastix, Protenterospora, Protomonas, Pseudoactiniscus, Pseudosporopsis, Rhizomonas, Rhynchodinium, Rigidomastix, Schewiakoffia, Sergentella, Serpentoplasma, Sphaerasuctans, Spongastericus, Spongocyclia, Stephanomonas, Strobilomonas, Tetradimorpha, Thaulirens, Topsentella, Toshiba, Trichonema, Urbanella.^[3]

See also

• Cavalier-Smith's system of classification
• Protist
• Protists in the fossil record

Notes

1. The first eukaryotes were “neither plants, animals, nor fungi”, hence as defined, the Protista would include the earliest common ancestor of all eukaryotes.
2. In the original 4-kingdom model proposed in 1959, Protista included all unicellular microorganisms such as bacteria.
3. This taxon belongs to the paraphyletic phylum Apusozoa Cavalier-Smith 1997 emend. 2013.^[18]
4. There are two competing phylogenetic hypotheses: Teretosporea (Corallochytrium + Ichthyosporea) and Pluriformea (Corallochytrium + Syssomonas).^[3] This article follows the latter hypothesis, because it is strongly supported by the most recent phylogenetic studies.^[13]
5. The term "Choanozoa" has been used since 1991 by Cavalier-Smith as a paraphyletic assemblage of opisthokont protists, and the terms "Apoikozoa" and "choanimal" were proposed as names for the clade Metazoa+Choanoflagellata. However, these terms have not been formally described or adopted, and were rejected in favour of a renamed Choanozoa to fit the clade Metazoa+Choanoflagellata.^[3]
6. The position of the genera Microcorycia, Parmulina, Penardochlamys and Zonomyxa, which were listed in 2002 under family Microcoryciidae, is not clear. They are placed here by morphological characters but this needs to be supported by molecular data.^[3]
7. The latest revision by Adl et al. (2019) ignores the grouping of some variosean genera into higher rank clades that was made in older studies because of the weakly supported SSU phylogenetic analyses, except for Fractovitellida, which is fully supported by phylogenomic analyses from 2017.^[3]
8. This order was initially divided into families, but phylogenetic analyses haven't supported the monophyly of each family. For this reason, in recent classifications there is no family rank division within it.^[29][3]
9. This genus grouped with Dermamoebidae in a phylogenetic anaysis that used a limited number of taxa.^[42] In the recent taxonomy it was listed as a separate clade until its position is better resolved.^[3] A 2023 analysis placed it, once again, related to Dermamoebida in a clade with Microglomus.^[43]
10. Both genera group together in some phylogenetic analyses, but usually appear separated. They were considered only a potential branch of Discosea, unless proven otherwise.^[3] A 2023 analysis places both genera in Flabellinia, closely related to Thecamoebida.^[43]
11. This genus could be a synonym of Vannella.^[3]
12. Latest analyses show that Microheliella is the sister group to Cryptista.^[14]
13. Telonemia is the sister group to the SAR clade.^[11]
14. The picobiliphytes are phylogenetically closer to Rhodophyta and Rhodelphis than to other groups, and are therefore considered part of Archaeplastida.^[49]
15. Within the order Anoecida, the four families Anoecaceae, Caecitellaceae, Cafeteriaceae and Symbiomonadaceae were included by T. Cavalier-Smith in 2006. In a 2013 revision, he simplified the classification by transferring Symbiomonadaceae and Anoecaceae to Cafeteriaceae.^[69] However, both of those families remain accepted by the scientific community as independent from Cafeteriaceae as of 2020.^[67]
16. Cavalier-Smith hypothesized in 2013 a sister relationship between actinophryids and raphidophytes, with both groups placed under the taxon Raphidomonadea. The molecularly uncharacterized genus Commation was classified as part of this taxon.^[69] However, the placement of actinophryids among ochrophytes is still unstable and uncertain,^[80][81] and Commation has never been included in classifications since.^{[citation needed]}
17. O'Kelly placed the genera Antarctosaccion, Chrysomeris, Chrysonephos, Nematochrysis/Chrysowaernella, Phaeosaccion and Rhamnochrysis in the order Chrysomeridales nomen nudum in 1989,^[83] and Cavalier-Smith placed it inside the class Chrysomeridophyceae (spelt originally as Chrysomerophycea) in 1995.^[84] However, the class was proven to be polyphyletic. As a result, some of its genera (Nematochrysis/Chrysowaerella) were transferred to the class Chrysoparadoxophyceae, while others (Antarctosaccion and Phaeosaccion) were transferred to the class Phaeosacciophyceae. Due to a lack of molecular data, the placement of Chrysomeris, Chrysonephos and Rhamnochrysis remains unknown.^[85]
18. The position of Eustigmatophyceae is still unstable, with different phylogenetic methodologies showing affinities to either of the SI and SII clades.^[87][81]
19. The taxonomic ranks above class level (phylum, subphylum, infraphylum, etc.) are unstable within the Alveolata, due to the many different existing classifications. For example, the phylum-level rank has been traditionally assigned to Perkinsozoa,^[101] Dinoflagellata, Chromerida and Apicomplexa, all of which have been classified as phylum Myzozoa,^[102] which in turn has been classified inside phylum Miozoa.^[74] Treating the four myzozoan groups as separate phyla is generally accepted among phycologists,^[103] while at the same time the rejection of higher taxonomic ranks due to being superfluous is prevalent among protistologists.^[3]
20. Apart from morphological descriptions, no molecular analysis has solidly affiliated Rastrimonas with the Perkinsozoa.^[104]
21. The genera Parallobiopsis, Ellobiocystis and Rhizellobiopsis are only provisionally placed among ellobiopsids.^[115]
22. Highly divergent 18S rRNA.^[3] Since 2020 member of newly identified major apicomplexan subgroup Marosporida, putting together Aggregata octopiana Frenzel 1885, Merocystis kathae Dakin, 1911 (both Aggregatidae, originally coccidians), Rhytidocystis sp. 1 and Rhytidocystis sp. 2 Janouškovec et al. 2019 (Rhytidocystidae Levine, 1979, originally coccidians, Agamococcidiorida), and Margolisiella islandica Kristmundsson et al. 2011 (closely related to Rhytidocystidae)^[120]
23. This taxon is artificial; many of the families listed in it are not monophyletic and have little support from phylogenetic analyses.^[3]
24. There is only one molecular sequence from this genus, which causes long branches in gene phylogenies, and the node is unresolved.^[3]
25. According to Nakamura & Suzuki, the only extant (i.e. not extinct) orders of Polycystinea are Spumellaria, Nassellaria, Collodaria and Orodaria. Therefore, Entactinaria is considered an exclusively fossil group.^[148]
26. The genus Tetragonidium is known only from one written diagnosis and some illustrations, and its affinities with Cryptophyceae are very uncertain.^[157]
27. Probably a synonym of the zygomycete fungus Nephridiophaga.^[3]
28. Labyrinthomyxa, a genus of putative labyrinthulomycetes, is placed incertae sedis because of limited data.^[188]
29. May be the same genus as Belonocystis.^[3]
30. It is not yet known whether this organism is an eukaryote or a prokaryote.^[189]