Genetically, they are categorized into three separate, but related groups: Ainu, Ryukyuan and Mainland (Yamato). According to modern genetic analyses, they primarily have Northeast Asian, East Asian, and to a lesser extent, heterogeneous Jōmon ancestries.[6][7]
Anthropologically, they are classified under the "Northeast Asian" cluster and show strong resemblance with Koreans[8][9] and to an extent, southern East Asian groups.[10][11]
Glacier cover in Japan at the height of the last glaciation about 20,000 years ago with the land bridge now gone.
A common origin of Japanese has been proposed by a number of scholars since Arai Hakuseki first brought up the theory and Fujii Sadamoto (藤井 貞幹), also known as Teikan Tou[ja] (藤 貞幹), a pioneer of modern archaeology in Japan, also treated the issue in 1781.[12] But after the end of World War II, Kotondo Hasebe[ja] (長谷部 言人) and Hisashi Suzuki[ja] (鈴木 尚) claimed that the origin of Japanese people was not the newcomers in the Yayoi period (300 BCE – 300 CE) but the people in the Jōmon period.[6] However, Kazuro Hanihara[ja] (埴原 和郎) announced a new racial admixture theory in 1984.[6] Hanihara also announced the theory "dual structure model" in English in 1991.[13] According to Hanihara, modern Japanese lineages began with Jōmon people, who moved into the Japanese archipelago during the Paleolithic. Hanihara believed that there was a second wave of immigrants, from Northeast Asia to Japan from the Yayoi period. Following a population expansion in Neolithic times, these newcomers then found their way to the Japanese archipelago sometime during the Yayoi period. As a result, miscegenation was common in the island regions of Kyūshū, Shikoku, and Honshū, but did not prevail in the outlying islands of Okinawa and Hokkaidō, and the Ryukyuan and Ainu people continued to dominate there. Mark J. Hudson claimed that the main ethnic image of Japanese people was biologically and linguistically formed from 400 BCE to 1,200 CE.[6] Currently, the most well-regarded theory is that present-day Japanese are descendants of both the indigenous Jōmon people and the immigrant Yayoi people.
Main migration routes into Japan during the Jōmon and Yayoi period.
On the other hand, a study published in October 2009 by the National Museum of Nature and Scienceet al. concluded that the Minatogawa Man, who was found in Okinawa and was regarded as evidence that the Jōmon people were not a homogenous group and that these southern Jōmon came to Japan via a southern route and had a slender and more neo-Mongoloid face unlike the Northern Jōmon.[14] Hiroto Takamiya of Sapporo University suggested that the people of Kyushu immigrated to Okinawa between the 10th and 12th centuries CE.[15][16] Regardless, both Northern and Southern Jōmon were craniofacially different from modern Mainland Japanese and had European-like features[17] and a 'well-defined and less flat upper face' respectively.[18] But they still had hair and teeth morphology that was characteristic of East Asian peoples, especially Northern Jōmon.[17]
A 2011 study by Sean Lee and Toshikazu Hasegawa[19] reported that a common origin of Japonic languages had originated around 2,182 years before present.[20]
A 2015 study revealed that modern Japanese possess 2.2% West Eurasian ancestry, which likely originated from interactions with Silk Road traders around 1700 years ago.[21]
Phylogenetic tree of Ainu, Ryukyuan, Mainland Japanese, and other Asian ethnic groups. The Ainu and the Ryukyuan were clustered with 100% bootstrap probability, followed by the Mainland Japanese. The three populations in the Japanese archipelago clustered with the Korean with 100% bootstrap probability.[22][23]
The modern Japanese cluster is said to be the most similar with the Korean one; in a haplotype-based study, the Japanese cluster was found to share 87–94% of its genetic components with the Korean cluster, compared with a Han Chinese result of only 0–8%, a distinct contrast. Moreover, the genetic affinity to the Korean cluster was particularly strong among a cluster hailing from Shimane specifically and Honshu more broadly, but relatively less pronounced, albeit still overwhelming, in the Kyushu clusters. In any case, however, the study clarifies that "the estimate of ancestry profile cannot provide the definitive history of original migration, unless it will be further verified against historical evidence."[8] Some studies suggest a genetic connection between Koreans and Southeast Asian populations. A 2017 study by Ulsan University analyzed a 7,700-year-old skull in Korea, finding evidence of genetic links to ancient populations, including those from Southeast Asia, such as Vietnamese people. This research highlights the complex migration patterns in East Asia’s prehistory.[24] Similarly, Japanese research conducted in 1999 proposed that the Yayoi people, an ancient population contributing to modern Japanese ancestry, may have migrated from the Yangtze River basin in southern China. This was supported by DNA analyses showing similarities between Yayoi remains in southwestern Japan and early Han Dynasty remains from China’s Jiangsu Province.[25] However, other studies suggest that modern Koreans share closer genetic ties with Central Asian and Northern East Asian populations. A mitochondrial DNA analysis revealed a genetic affinity between Koreans and Mongolians, indicating a shared Central Asian ancestry. Additionally, genetic research suggests that while Koreans share some common ancestry with other East Asian populations, their genetic ties with the Chinese are relatively more distant.[26] Genome-wide studies further demonstrate that Koreans are genetically closest to Yamato Japanese and Manchu populations, reflecting shared ancestry and historical interactions, while genetic connections between Koreans and Southeast Asians are more limited.[27][28]
A population genomic PCA graph, showing the substructure of Eastern Asian populations, including analyzed Japanese Jōmon samples. Japanese people's cluster (squares) is almost indistinguishable to the Korean people's cluster (circles), while the Jōmon samples are shifted towards the Siberian cluster in a more distinct position.[29] (2020)The origins of the Jōmon and Yayoi people have often been a subject of dispute, and a recent Japanese publisher[30] has divided the potential routes of the people living on the Japanese archipelago as follows:
Aboriginals that have been living in Japan for more than 10,000 years. (Without geographic distinction, which means, the group of people living in islands from Hokkaido to Okinawa may all be considered to be Aboriginals in this case.)
Immigrants from the northern route (北方ルート in Japanese) including the people from the Korean peninsula, mainland China and Sakhalin Island.
A study in 2017 estimates the Jōmon ancestry in people from Tokyo at approximately 12%.[36]
In 2018, an independent research conducted by director Kenichi Shinoda[ja] (篠田 謙一) and his team at National Museum of Nature and Science was broadcast on NHK Science ZERO and it was discovered that the modern day Japanese are genetically extremely close to the modern day Koreans.[37] A genome study (Takahashi et al. 2019) shows that modern Japanese (Yamato) do not have much Jōmon ancestry at all. Nuclear genome analysis of Jōmon samples and modern Japanese samples show strong differences.[38] Various studies estimate the proportion of Jōmon ancestry in Japanese people at around 9-13%, with the remainder derived from later migrations from Asia including the Yayoi people.[36][39][40]
Ancestry profile of Japanese genetic clusters illustrating their genetic similarities to five mainland Asian populations.[41]
Gyaneshwer Chaubey and George van Driem (2020) suggest that the Jōmon people were rather heterogeneous, and that there was also a pre-Yayoi migration during the Jōmon period, which may be linked to the arrival of the Japonic languages, meaning that Japonic is one of the Jōmon languages. This migration is suggested to have happened before 6000BC, thus before the actual Yayoi migration.[42]
According to Alexander Vovin, the Yayoi were present in the central and southern parts of Korea before they were displaced and assimilated by arriving proto-Koreans.[47][48] A similar view was raised by Whitman (2012), further noting that the Yayoi are not closely related to the proto-Koreanic speakers and that Koreanic arrived later from Manchuria to Korea at around 300 BC and coexisted with the Japonic speakers. Both had influence on each other and a later founder effect diminished the internal variety of both language families.[49]
Jared Diamond, the author of Guns, Germs, and Steel, suggested that the Yayoi period in Japan was initiated by immigrants from the Korean peninsula. Citing research findings, he stated that Yayoi Japan likely received millions of immigrants from Korea. These immigrants, during the Yayoi transition, are believed to have overwhelmed the genetic contribution of the Jōmon people, whose population was estimated to be around 75,000 at that time.[50]
Recent full genome analyses by Boer et al. 2020 stated that the Jōmon did not show high affinities with Basal Asians like Hoabinhians or Tianyuan Man but are also diverged from mainland East Asians since the Paleolithic. They also have high affinities with coastal East Asians, including Austronesians and Siberians, suggesting admixture.[12][51] According to Gakuhari et al. (2020), these coastal East Asian affinities can be explained by shared ancestry rather than actual admixture.[52]
According to a March 2021 study on genetic distance measurements from a large scale genetic study titled 'Genomic insights into the formation of human populations in East Asia', the modern "Japanese populations can be modelled as deriving from Korean (91%) and Jōmon (9%)."[9]
A 2025 study by Kim et al. states that the Yayoi population, represented by the Doigahama Yayoi individual, was closely related to the Korean_Ando population. The Doigahama Yayoi individual can be modeled as having 7% Jomon-related, 67% East Asian-related, and 26% Northeastern Siberian-related ancestries, with East Asian-related ancestry being represented by present Koreans rather than Han Chinese. No other modern population is as closely related to this individual as modern Japanese and Koreans.[53]
Tripartite ancestry theory
A September 2021 study published in the journal Science Advances proposed that the people of Japan bore genetic signatures from three ancient populations rather than just two as previously thought.[54]
Proposed tripartite styled genomic transitions in parallel with cultural transitions in pre- and protohistoric Japan. (2021)The study states that in addition to the previously discovered Jōmon and Yayoi strands, a new strand was hypothesized to have been introduced, most likely from the southern Korean peninsula, during the Yayoi-Kofun transition period, where there was strong cultural and political affinity with Korea and China.[54] According to the study, the genetic profile of the Japanese population was established in the Kofun period. It is said that the Kofun strand in modern-day Japanese was concentrated in specific regions such as Kinki, Hokuriku and Shikoku.[55] Over 70% of their genetic makeup can be attributed to the Kofun component, with 15-20% being attributed to Yayoi and the rest to the Jōmon component.[54]
However, the same paper later reiterated that the Yayoi show excess affinities to populations with no cultural relations to rice farming such as those from the West Liao River basin in Northeast China, Baikal, and Northeast Siberia. No significant affinities to Yellow River populations were likewise found. The research also found that rice farming was introduced to Japan from the Shandong peninsula to the Liaodong Peninsula and finally to the Korean peninsula, where it was directly spread to Japan.[54]
Rui Wang (王瑞) and Chun-Chao Wang (汪群超) (2022) reiterated that Yayoi immigrants did not demographically replace the Jōmon. Instead, they co-existed and intermarried with indigenous Jōmon, which led the Yayoi to have 60% Jōmon ancestry. The rest was Northeast Asian. Jōmon admixture was decreased when ancestries related to the Northern Han Chinese (Yellow River ancestry) were introduced in the Kofun period.[56]
They later clarified in another paper (2023) that overall, modern Japanese cluster with the "Korean_Antu" population, covering Koreans from Antu County, who share more genetic drift with Koreans, Han Chinese, Hmong-Mien and Tai-Kadai.[57]
Xiaoxi Liu (刘小晰) et. al (2024) stated that Jōmon admixture in contemporary Japanese people varies depending on region, with admixture being the highest in southern Japan, especially Okinawa (28.5%), followed by northeastern Japan (19%) and western Japan (12%). They also noted that the East Asian strand (labelled "Kofun") was dominant in western Japan while the Northeast Asian strand was dominant in northeastern Japan.[58] Interestingly, Liu's research indicates a diminished number for the Kofun strand which was originally thought to have been over 70% in the previous papers (2021-2022), down to at most 35%. The rest consists of the aforementioned Jōmon strand and the northeastern strand labelled as "Three Kingdoms Korea" in the study, depending on the region.[58]
However recently, the tripartite ancestry theory is being met with criticism since its introduction in 2021. In essence, Japanese researchers claim that a tripartite theory is redundant as the genealogical difference between Yayoi and Kofun groups is not significant enough and that the temporal discrepancy of the periods is minuscule. Japanese linguists also state that the languages spoken during the periods are generally related to each another and that the speakers were most likely related.
According to Pere Gelabert in a 2022 paper, ancient Koreans of the Three Kingdoms period of Korea coded "Korea TK", bore close genetic similarity with Kofun period Japanese people. In particular, "Korea-TK_2" is closely related to "present-day Japanese, the ancient Kofun, and other ancient Japanese populations with Jomon ancestry" due to their higher Jōmon-like ancestry. "Korea-TK_2" can be modeled as having 66% ± 7% Bronze Age West Liao River-related ancestry and 34% ± 7% Jōmon-related ancestry. Or 32% Northeast Asian, 43% Han, and 25% Japan Jōmon. In terms of the Japanese Kofun population, they could be modeled as having 71% ± 10% "Korea-TK_2"-related ancestry and 29% ± 10% Late Bronze Age to Iron Age Yellow River-related ancestry.[59]
A study published in April 2024 by Hisashi Nakao (中尾 央), claims that the Kofun strand had much overlap with the previous Yayoi strand and that the two strands were genealogically closer than that of the Jōmon group.[60] Nakao stated that "[the results] suggest that the Jōmon people were rather different from the Yayoi and Kofun people in the facial height and the anterior–posterior length [...] indicating that temporal differences are not significant among the Yayoi and Kofun periods. [...] the large overlap in morphological variation between the Yayoi and Kofun people could be an important step in further research."[60] The research also boasts of using the largest Kofun samples to date.[60]
A recent study published by the University of Tokyo in October 2024 also refuted the tripartite origin theory,[61] claiming that the Kofun strand was not a single strand that was introduced separately into Japan, but a strand that was part of an already existing group within the Korean peninsula.[62] According to the study, late-Yayoi period individuals carried both Yayoi and Kofun DNA, supporting Nakao's theory of lack of temporal differences between the two periods. The lead researcher and professor at the University of Tokyo's Department of Biological Sciences, Jun Ohashi (大橋 順) spoke with Science Daily,[4] further explaining the new findings and criticizing the previous assumption. "Our results suggest that between the Yayoi and Kofun periods, the majority of immigrants to the Japanese archipelago originated primarily from the Korean peninsula," says Ohashi. "The results also mean the three-way admixture model, which posits that a Northeast Asian group migrated to the Japanese archipelago during the Yayoi period and an East Asian group during the Kofun period, is incorrect."[4]
A recent interview with the director of the National Museum of Nature and Science, Kenichi Shinoda[ja] (篠田 謙一) in December 2024 summarized the current consensus in regards to the genomic makeup of the modern Japanese. Shinoda stated that over 90% of the modern Japanese DNA derives from an ancient strand that originated at an area near the Liao River around 50,000 years ago, where it was then introduced to the Korean peninsula (which in turn mixed with the Southern Jōmon-like inhabitants) and 10,000 years later was introduced into the Japanese archipelago.[5] Shinoda also remarked that these migrations happened throughout the later Yayoi period and that the Japanese genes remained homogenous since then, stating that "the genetic makeup of the ancient Yayoi people and us (Yamato people) are almost identical".[5] The director did not mention "Kofun", but insisted on calling the later settlers as "Toraijin (Immigrants)" or more specifically "late-Yayoi period settlers", despite taking part in previous studies surrounding the strand and mentioning it at the time of its proposal.[63]
Jonghyun Kim et al. (2025) states that the Kofun population shares the same Koreanic origins as the Yayoi population and has similar ancestral proportions to those found in the Doigahama Yayoi, who represents the Yayoi population. East Asian ancestry, represented by present Koreans, was also predominantly found in both populations.[53]
Linguist, author, and lecturer Makoto Mogi[ja] (茂木 誠) (2025) insisted that the immigrants with the "East Asian ancestry" were ethnically different from the Han Chinese having come from the north and being linguistically different.[64] According to Mogi, East Asian ancestry immigrants such as Empress Jingū's ancestor, Amenohiboko and other famous Kofun period immigrants, were most likely proto-Koreanic speakers due to the similarities in grammar with modern Korean,[65][64] an argument made similar by fellow linguist Alexander Vovin.[66] Mogi posited that these proto-Koreanic speakers entered the peninsula by replacing or absorbing the pre-existing Peninsular Japonic speaking natives (Southern Jōmon-like inhabitants) before entering Japan,[64] an argument that aligns closely with the anthropological argument made by aforementioned Kenichi Shinoda (2024).[5]
The migration routes of proto-Japonic and proto-Koreanic speakers.[67] (2022)A similar observation was made previously by Kazuo Miyamoto[ja] (宮本 一夫), a renowned linguist and emeritus professor at Kyushu University in 2022. Miyamoto noted that "Central Japanese was heavily influenced by Old Korean (possibly through Baekje) during the Kofun and Asuka periods, from the 4th to 7th centuries AD"[68] which supports Mogi and Vovin's assumptions. He linked the Yayoi period with the Mumun period of Korea and stated that the proto-Japonic language was spread during this time.[69][68] He also remarked that the proto-Japonic of the Yayoi/Mumun period and proto-Koreanic that was introduced during Kofun/Asuka period stemmed from the same ancestral language, stating that "the homeland of both languages is the same based on archeological evidence, and they are kindred language families"[68] and that "Proto-Japonic and Proto-Koreanic split off from the Transeurasian languages in southern Manchuria"[68] positing that the Yayoi (proto-Japonic) and Kofun (proto-Koreanic) migrations were heavily related, a conclusion made similar to Hisashi Nakao (2024).
Rajvir Yadav et al. (2000) stated the sitting height to stature ratios of different populations: South Indian (0.4922), female Indian (0.4974), Eastern Indian (0.4991), Southeastern African (0.5096), Central Indian (0.5173), US (0.5202), Western Indian (0.5243), German (0.5266) and Japanese (0.5452).[72]
Hirofumi Matsumura et al. (2001) and Hideo Matsumoto et al. (2009) said that the Japanese and Vietnamese people are regarded to be a mix of Northeast Asians and Southeast Asians. However, the amount of Northern genetics is higher in Japanese people compared to Vietnamese, who are closer to other Southeast Asians (Thai or Bamar people).[73][74]
Neville Moray (2005) said that, for Korean and Japanese pilots, sitting height is more than 54% of their stature, with about 46% of their stature from leg length. Moray said that, for Americans and most Europeans, sitting height is about 52% of their stature, with about 48% of their stature from leg length. Moray indicated that modifications in basic cockpit geometry are required to accommodate Japanese and Vietnamesepilots. Moray said that the Japanese have longer torsos and a higher shoulder point than the Vietnamese, but the Japanese have about similar arm lengths to the Vietnamese, so the control stick would have to be moved 8cm closer to the pilot for the Japanese and 7cm closer to the pilot for the Vietnamese. Moray said that, due to having shorter legs than Americans, rudder pedals must be moved closer to the pilot by 10cm for the Japanese and 12cm for the Vietnamese.[75]
Ann Kumar (1998) said that Michael Pietrusewsky (1992) said that, in a craniometric study, the cranial bones of Southeast Asians (Borneo, Vietnam, Sulu, Java, and Sulawesi etc.) are closer to Japanese, in that order, than Mongolian and Chinese populations are close to Japanese. In the craniometric study, Michael Pietrusewsky said that, even though Japanese peoplecluster with Mongolians, Chinese and Southeast Asians in the larger Asian cluster, the cranial bones of Japanese people are more closely aligned with several Mainland and Island Southeast Asian samples than with Mongolians and Chinese. However, Pietrusewsky also said, more research is needed on the similarity of the cranial bones between Japanese and Southeast Asians.[78][79]
In a 1994 craniometric study, Pietrusewsky found that the Japanese series, which was a series that spanned from the Yayoi period to modern times, formed a single branch with Korea. Later, Pietrusewsky (1999) found, however, significant differences between the Korean and Yayoi people in the East Asian cluster, indicating that the connection that Japanese have with Korea would not have derived from Yayoi people.[10]
However, in a follow-up study, Pietrusewsky (2010) corrected that East Asians and Southeast Asians were markedly separated from each other. He found that Koreans had the most similar cranial bones to ancient and modern Japanese including the Yayoi people and Jōmon people. Japanese cranial series also resembled those of Atayal, which was similarly observed for Koreans, Hainanese and Taiwanese.[11] He stated that a common origin of Northeast Asians could be traced and that they began entering the Japanese archipelago at the beginning of the Yayoi period.[11]
Park Dae-kyoon et al. (2001) said that distance analysis based on thirty-nine non-metric cranial traits showed that Koreans are closer craniometrically to Kazakhs and Mongols than to the populations in China and Japan.[80]
Enfield (2011) sees phenotypic similarities between present Japanese populations and Dong Son populations from northern Vietnam and Neolithic populations from southern China. Based on dental analyses, they were Australo-Melanesians who heavily mixed with migrants related to ancient Chinese populations, affecting them genetically and phenotypically.[81]
Dudzik (2015) states that southern Japanese are morphologically the most similar to Jōmon and Ainu groups, as well as Yayoi groups. Conversely, northern Japanese are significantly more influenced by northeast Asian groups due to external migration from the north since the fifth century or earlier. This also affected subpopulations like Ainu, suggesting that 'parental population traits' were better preserved in the southernmost parts of the Japanese archipelago.[82]
According to Watanabe et. al (2021), contemporary Kinki populations phenotypically differ the most from Jōmon people, especially Hokkaido Ainu. Other Japanese subpopulations were more intermediate although morphological similarities exist between Hokkaido Ainu and contemporary Tohoku populations.[83]
Torimitsu et. al (2024) states that there is quantifiable dimorphism in the cranium of Japanese people, similar to Thais, Indonesians, Filipinos and Malays.[84] Japanese skulls also share some similarities with Hispanics and Filipinos,[85] implied by the frequency of Hispanic skulls from southwestern United States being misclassified as Asian, particularly Japanese and Filipino.[85][84] However, Japanese craniums can be distinguished from Filipino craniums, with the former having higher upper facial height and shorter inferior malar lengths on average.[86] Nasal height and breadth were also greater and smaller than those found in Filipino craniums respectively although Thai craniums exhibited greater nasal height and breadth than those found in Japanese craniums.[84] Japanese craniums also greatly differ from populations like 'typical' Western Australians, with the latter having longer and taller skulls and narrower frontal bones. On average, they also have greater maximum cranial length and basion-nasion length and lower mastoid height.[87]
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