In population genetics, extensive research has been done on the genetic origins of modern Japanese people.
Historically, Japanese people possess ancestries introduced during the Jōmon period, Yayoi period, and arguably, the Kofun period. These genetic markers are best represented by the Jōmon, Yayoi, and Toraijin peoples respectively.
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.
Anthropologically, they are classified under the "Northeast Asian" cluster and show strong resemblance with Koreans, and to some extent, southern East Asian groups.
Origins
Dual ancestry theory
A common origin of the Japanese people has been proposed by a number of scholars since Arai Hakuseki first brought up the theory. Fujii Sadamoto (藤井 貞幹), also known as (藤 貞幹), a pioneer of modern archaeology in Japan, also treated the issue in 1781.Miller, Roy A. The Japanese Language. Tokyo: Charles E. Tuttle. 1967, pp. 61-62 After the end of World War II, (長谷部 言人) and Hisashi Suzuki [ja] (鈴木 尚) claimed that Japanese people originated from the peoples of the Jōmon period instead of newcomers from the Yayoi period (300 BCE – 300 CE).
(埴原 和郎) announced a new racial admixture theory in 1984. Hanihara also announced the theory "dual structure model" in English in 1991. 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 during the Yayoi period.
Following a population expansion in Neolithic times, these newcomers 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. Currently, the most well-regarded theory is that present-day Japanese have dual descent from the indigenous Jōmon people and the immigrant Yayoi people.
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. 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, 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."
A 2011 study by Sean Lee and Toshikazu Hasegawa reported that a common origin of Japonic languages had originated around 2,182 years before present. According to a 2015 study, modern Japanese possess 2.2% West Eurasian ancestry, which likely originated from interactions with Silk Road traders around 1700 years ago. A study in 2017 estimates the Jōmon ancestry in people from Tokyo at approximately 12%. 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 close to the modern day Koreans. A genome study (Takahashi et al. 2019) shows that modern Japanese (Yamato) do not have much Jōmon ancestry at all. Nuclear genome analyses of Jōmon samples and modern Japanese samples show strong differences. 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. 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%)."
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.
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.
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. 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. According to a 2023 study, the Hondo Japanese are genetically intermediate between the Chinese/Korean and Ryukyuan clusters.Some theories propose that the Yayoi people introduced wet rice cultivation to Japan from the Korean peninsula and Jiangnan near the Yangtze River Delta in ancient China. Additionally, some scholars suggest that the Yayoi and their ancestors, the Wajin, may have originated from areas like Yunnan province in southern China.鳥越憲三郎『原弥生人の渡来』(角川書店,1982)、『倭族から日本人へ』(弘文堂 ,1985)、『古代朝鮮と倭族』(中公新書,1992)、『倭族トラジャ』(若林弘子との共著、大修館書店,1995)、『弥生文化の源流考』(若林弘子との共著、大修館書店,1998)、『古代中国と倭族』(中公新書, 2000)、『中国正史倭人・倭国伝全釈』(中央公論新社, 2004) Suwa Haruo argued that Wa-zoku (Wajin) might have been related to the Baiyue (百越).諏訪春雄編『倭族と古代日本』(雄山閣出版、1993)また諏訪春雄通信100
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. 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 influenced each other and a later founder effect diminished the internal variety of both language families. 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-era 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. According to a 2020 study, Japanese exhibit high genetic similarities with Koreans and inherited their East Asian-related components during the Yayoi period. Proto-Koreans received genetic input from Siberian-related and Austroasiatic-related populations, along with combined Vat Komnou-related and Nui Nap-related sources from Southern China after the Bronze Age, which shaped the genetic variation of modern Koreans by over 70%. Other studies also show this Southeast Asian contribution in proto-Koreans. Miyamoto (2022) states that proto-Japonic and proto-Koreanic shared a common origin in the eastern Liaoxi district of southern Manchuria. Proto-Japonic-speaking peoples migrated to Korea first and were associated with Mumun populations, who were influenced by Pianpu culture from the Liaodong district and rice-farming Shandong populations.
Ishiya et al. (2024) states that present Japanese and Koreans possess genetic components related to Ancient Northeast Asians (ANA), especially those from Mongolia and the Baikal region. Yayoi individuals were also closely related to Middle Neolithic individuals from Inner Mongolia, Miaozigou and the Haminmangha site, as well as Early Neolithic individuals (Xiaojingshan and Boshan) from Shandong, China. They also share Papuan-like components with the Jōmon people but this might reflect a different diverged East Eurasian lineage shared with other Asians. Kim et al. (2024) states that the Yayoi have the highest genetic affinities to the ancient "Korean_Ando (Antu)" population and drift further away from other contemporary Korean populations, like those from Gunsan and Gimhae. A previous study by Robbeets (2021) states that the Middle Neolithic "Korean_Ando" population derive 100% of their ancestry from Hongshan culture-related populations. However, they model the Yayoi as having mostly Upper Xiajiadian-related ancestry, which is disputed by other researchers, who believe that the Yayoi/Mumun peoples do not have exceptionally close ties with Upper Xiajiadian-related ancestry and can also be modeled with Hongshan-related ancestry. Yu et al. (2025) suggested that there was a genetic contribution from ancient Liaodong Peninsula populations to the ancestors of modern Japanese and Koreans. The study tentatively theorized that the Yellow River farmers descendants subjugated the previous Liaodong populations, forcing the elite Liaodong individuals such as Gao Bin (高賓) to attain more Yellow River ancestry while the native Liaodong agricultural populations moved towards Korea and Japan after the Warring States period.
Tripartite ancestry theory A September 2021 study published by Cooke et al. in Science Advances proposed that the people of Japan bore genetic signatures from three ancient populations rather than just two as previously thought.
Cooke at al. states that in addition to the previously discovered Jōmon and Yayoi components, a new component (i.e. Kofun) 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. According to Cooke et al., the genetic profile of the modern Japanese population was established in the Kofun period. The Kofun component, however, is specifically concentrated in Kinki, Hokuriku and Shikoku. Overall, the average modern Japanese derives over 70% of their ancestry from the Kofun component, with 15-20% being derived from the Yayoi component and the rest from the Jōmon component. The study's authors also note that modern Japanese have slightly more East Asian ancestry than Kofun peoples. Cooke et al. hypothesized that the Kofun component was related to ancient Yellow River populations from the Late Bronze Age to Iron Age, who themselves had 40% Northeast Asian ancestry and 60% East Asian ancestry. The same paper showcased that the Yayoi component has 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. Cooke et al. 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.