- Ellipsomyxa gobii Køie, 2003 (type)[1]
- Ellipsomyxa syngnathi Køie & Karlsbakk, 2009[2]
- Ellipsomyxa fusiformis Davis, 1917[3]
- Ellipsomyxa manilensis Heiniger & Adlard, 2014[4]
- Ellipsomyxa apogoni Heiniger & Adlard, 2014[4]
- Ellipsomyxa adlardi Whipps & Font, 2013[5]
- Ellipsomyxa arothroni Heiniger & Adlard, 2014[4]
- Ellipsomyxa mugilis Sitjà-Bobadilla & Alvarez-Pellitero, 1993[6]
- Ellipsomyxa gobioides Azevedo, Videira, Casal, Matos, Oliveira, Al-Quraishy & Matos, 2013[7]
- Ellipsomyxa kalthoumi Thabet, Tlig-Zouari, Al Omar & Mansour, 2016[8]
- Ellipsomyxa nigropunctatis Heiniger & Adlard, 2014[4]
- Ellipsomyxa arariensis Da Silva, Matos, Lima, Furtado, Hamoy & Matos, 2018[9]
- Ellipsomyxa amazonensis Zatti, Atkinson, Maia, Correa, Bartholomew & Adriano, 2018[10]
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