The Jōmon people represent the descendants of
Upper Paleolithic inhabitants from the Japanese archipelago, who became isolated from other mainland Asian groups about 22,000 to 25,000 years ago. They have been described as "one of the most deeply diverged populations in East Asia".
Genetics The Jōmon lineage is inferred to have diverged from Ancient East Asians between 25,000 to 38,000 years ago, after the divergence of the Basal East Asian
Tianyuan and
Hoabinhian lineages, but before Ancient East Asians split into
Ancient Northern East Asians and
Ancient Southern East Asians. Like other East Asian populations, the ancestors of the Jōmon people are suggested to have originated from Southeast Asia and expanded northwards to East Asia via both an interior and a coastal route. They represent one of the "earliest waves of migration". Some studies model the Jōmon lineage as a mixture of
Onge-related (44%) and Tianyuan-related (56%) ancestries or as a mixture of Onge-related (51.6%) and Early Neolithic Xiaogao-related (48.4%) ancestries, with the latter having Tungusic affinities. Other studies state that the Jōmon share ancestral components with the Yokchido individual from ancient Korea as well as Asian populations from the southern hemisphere. The latter ancestral component, however, is maximized in Papuans and Vanuatuans. Alternatively, the Jōmon lineage can be modeled as a relatively unadmixed lineage. Subsequent studies found that Hoabinhians are an unlikely source for deeper ancestry in the Jōmon. Instead, a yet unidentified deep East Asian source is suggested. Overall, Jōmon ancestry consistently forms a clade with Ancient Northern and Southern East Asians. They diverged from Ancient East Asians around the same time as the
Longlin specimen from Guangxi, China although other studies show an earlier divergence date for the latter. The Jōmon likewise diverged from Ancient East Asians much later than the basal Asian Xingyi_EN lineage found in Yunnan, China. According to Wang et al. (2025), the ancestors of Ancient East Asians were a mixture of Tianyuan-related and Xingyi_EN-related lineages. The Jōmon also exhibit a high degree of genetic homogeneity, which is attributed to "strong bottleneck and small effective population size". Beyond their
genetic affinities with other East Eurasian lineages, the Jōmon display weak but marginally relevant genetic affinity with the
Yana Rhinoceros Horn Site specimen, associated with
Ancient North Eurasians (or Ancient North Siberians). This indicates
gene flow between Ancient North Siberians and the ancestral Jōmon prior to the Jōmon's isolation from other East Eurasians. This gene flow is also associated with the introduction of
microblade technology to Northern Japan. According to Bennett et al. (2024), the Basal Asian-like ancestors of the Jōmon may have interacted with groups that entered Siberia through a northern migration route, thus explaining the observed affinities between the Jōmon and Ancient North Siberians. Other studies found no evidence for ANE-related gene flow or speculated that it was indirectly introduced via admixture with Northern East Asian populations that were admixed with ANE groups themselves. These affinities imply later contact episodes between the Jōmon and other East Eurasian populations but the direction of gene flow is unclear. Overall, the Jōmon are not closely related to most Asian populations besides modern Japanese and
Ulchi. Full genome studies on multiple Jōmon remains revealed them to carry gene alleles associated with a higher alcohol tolerance,
wet earwax, no derived variant of the
EDAR gene, and that they likely frequently consumed fatty sea and land animals. They also carried alleles for medium to light skin, dark and fine/thin hair, and brown eyes. Some samples also displayed a higher risk of developing
liver spots as a result of excessive sun exposure. Genetic data further indicates that the Jōmon peoples were genetically predisposed for higher triglyceride and
blood sugar levels, increasing the risk of obesity. At the same time, it gave them resistance to starvation. Modern Japanese share these alleles with the Jōmon period population, although at lower and variable frequency, in line with the inferred admixture among modern Japanese peoples. Watanabe et al. stated that the genetic predisposition for shorter stature among Japanese people often correlates with high Jōmon ancestry, with the opposite correlating with high continental East Asian ancestry.
Haplogroups It is thought that the haplogroups
D-M55 (D1a2a) and
C1a1 were frequent among the historical Jōmon period people of Japan. One 3,800-year-old Jōmon man excavated from
Rebun Island was found to belong to Haplogroup D1a2b1(D-CTS 220). Today, haplogroup D-M55 is found in about 35% and haplogroup C1a1 in about 6% of modern
Japanese people. D-M55 is found regularly only in Japanese (
Ainu,
Ryukyuans, and
Yamato) and Koreans (albeit with much lower frequency). D-M55 also has been observed in
Micronesia 5.1%,
Timor 0.2%, China 0–0.4%, this is explained by recent admixture, dating back to the
Japanese empire (1868–1945) occupation of those regions. A 2021 study estimated that the frequency of the D-M55 clade increased during the late Jōmon period. The divergence between the D1a2-M55 and the D1a-F6251 subclades (the latter of which is common in
Tibetans, other
Tibeto-Burmese groups, and
Altaians, and has a moderate distribution in the rest of East Asia, Southeast Asia, and Central Asia) may have occurred near the
Tibetan Plateau. Studies published in 2004 and 2007 show the combined frequency of M7a and N9b observed in modern Japanese to be from 12~15% to 17% in mainstream Japanese.
N9b is frequently found among the Hokkaido Jōmon while
M7a is found frequently among the Honshu Jōmon. However N9b is found only at very low percentage among the Honshu Jōmon. Haplogroup M7a now has its highest frequency in
Okinawa. Using the
Fossa Magna as the boundary line, M7a was more common in western Jōmon while N9b was more common in eastern Jōmon, which can be explained by genetic drift rather than different genetic backgrounds for various Jōmon settlers. Other studies state that M7a was present at all sites in Early Jōmon Japan, whether northern or southern, although N9b was not found at any site below Kyushu. In Middle Jōmon Japan, M7a and N9b were both observed, especially at the Chiba Prefecture. In Late Jōmon Japan, M7a was present in Hokkaido and Okinawa. N9b was common in Funadomari while D4b2 and D4h2 were common in the Shomyoji shell midden and Funadomari respectively. In the Final Jōmon, N9b prevailed in Hokkaido while N9b and M7a were both observed in Honshu. The following sites in Hokkaido have these common haplogroups; G1b at Usu-Moshiri, G1b and D4h2 at Usu-Moshiri, G1b at Minami-Usu 6 and D4h2 at Onkoromanai. According to a 2025 study, haplogroup M7 diverged into M7a and M7b'c, which further split into M7b and M7c, with the latter two being common in Southern East Asia.
Morphological characteristics ). Exhibition in National Museum of Nature and Science.Although there is regional variance among different Jōmon remains, they displayed an overall coherent morphology. Historically, the Jōmon people were classified as "
South Mongoloid" or "
Proto-Mongoloid"; displaying specific affinities with Native Americans and to an extent,
Negrito samples. They broadly resemble groups such as "[...] Southeast Asians, Upper Paleolithic Asians, or Northeastern Asians, as well as present-day indigenous populations of the Ainu of Hokkaido and Ryukyu Islanders", as well as
Cro-Magnon populations. and to an extent, colder climates. Close morphological similarities also exist between the Jōmon people and the ~33,000 to 23,000 years old
Liujiang man from
Guangxi, China and the
Minatogawa Man from
Okinawa. The Jōmon also display phenotypic affinities with putative
Australo-Papuan groups, specifically prehistoric populations from Southern East Asia, such as the Hoabinhian hunter-gatherers, and Northern China, such as the Upper Paleolithic
Zhoukoudian remains. They possessed traits such as 'dolichocephalic calvaria, large zygomatic bones, remarkably prominent glabellae and superciliary arches, concave nasal roots, and low and wide faces', yet were genetically closer or ancestral to later East Asians despite phenotypic discontinuities. These Paleolithic variations were lost in modern Eastern Asian populations due to long-term demographic replacement.
Dental morphology suggests that the Jōmon had
Sundadont dental structure, which is more common among modern Southeast Asians and indigenous Taiwanese. Sundadonty is ancestral to the Sinodont dental structure commonly found among modern Northeast Asians, suggesting that the Jōmon split from the common "Ancestral East Asians" prior to the formation of modern Northeast Asians. Chatters, citing anthropologist C. Loring Brace, classified Jōmon and Polynesians as a single craniofacial "Jōmon -Pacific" cluster. Chatters, citing Powell, noted that the Jōmon most resembled the Native American Kennewick Man and Polynesians. According to him, the Ainu descend from the Jōmon people, an East Asian population with "closest biological affinity with south-east Asians rather than western Eurasian peoples". Kondo et al. analyzed the regional morphological and
craniometric characteristics of the Jōmon-era population of Japan, and found that they were morphologically heterogeneous and displayed differences along a Northeast to Southwest cline. Differences were based on the
cranial index, with Hokkaido Epi- Jōmon crania being mesocephalic and Okinawan crania being brachycephalic. They concluded that the "Jōmon skulls, especially in the neurocranium, exhibit a discernible level of northeast-to-southwest geographical cline across the Japanese archipelago, placing the Hokkaido and Okinawa samples at both extreme ends. The following scenarios can be hypothesized with caution: (a) the formation of Jōmon population seemed to proceed in eastern or central Japan, not western Japan (Okinawa or Kyushu regions); (b) the Kyushu Jōmon could have a small-sized and isolated population history; and (c) the population history of Hokkaido Jōmon could have been deeply rooted and/or affected by long-term extrinsic gene flows." They also suggested that regional differences in cranial length is based on environmental effects. According to a 2023 study, there were no significant differences in craniofacial or facial shapes within the Jōmon. However, Southern and Western Jōmon often have more globular neurocraniums when viewed in the sagittal plane compared to Northeastern Honshu Jōmon, who often have high and large frontal regions, along with low, more compressed and angled occipital regions. This reflects a shift towards agricultural lifestyles among Southern and Western Jōmon whilst older forager lifestyles were upheld by Northeastern Honshu Jōmon. Jōmon from Southern and Western Japan and inland central Honshu also differ from Jōmon from coastal central Honshu, Northeastern Honshu and Hokkaido in terms of their temporalis muscle region, reflecting differential influences of plant-based and marine-based diets respectively. The former Jōmon group are described as having "an anteroposteriorly shorter, superoinferiorly taller temporalis region with a mediolaterally narrower temporal fossa". A 2025 study shows no significant inter-phase or geographical differences among different Jōmon specimens. However, variations within phases and geographical regions are more salient. Craniofacial features of the Jōmon people were significantly retained by the Ainu and Okinawans/Ryukyuans. The Ainu have 2 genes "associated with facial structure in Europeans" but still possessed hair and teeth morphology found in East Asians. In regards to facial flatness, the Ainu were intermediate between
Caucasoids and
Mongoloids but another study states that they were well within the Mongoloid range. Ainu also exhibit strong influence from Northeast Asian populations. Meanwhile, Okinawans/Ryukyuans have a "well-defined and less flat upper face", which is characterized by a prominent
glabella and
nasal root.
ATL retrovirus A gene common in Jōmon people is a retrovirus of
ATL (human T lymphotropic virus, HTVL-I). This virus was discovered as a cause of
adult T cell leukemia (ATL), and research was advanced by Yorio Hinuma of
Kyoto University Virus Research Institute. Although it was known that many virus carriers existed in Japan, it was not found at all in neighboring countries of East Asia. Meanwhile, it has been found in many
Africans,
Native Americans,
Tibetans,
Siberians, Burmese people,
Indigenous people of New Guinea, Polynesians, etc. Looking at distribution in Japan, it is seen particularly frequently in southern
Kyushu,
Nagasaki Prefecture,
Okinawa and among the
Ainu. And it is seen at medium frequency in the southern part of
Shikoku, southern part of the
Kii Peninsula, the Pacific side of the
Tōhoku region (
Sanriku) and
Oki Islands. Overall, carriers of the ATL retrovirus were found to be more common in remote areas and remote islands. When examining the well-developed areas of ATL in each region of Kyushu, Shikoku, and Tōhoku in detail, carriers are preserved at high rates in small settlements that were isolated from the surroundings and inconvenient for traffic. Based on the above, Hinuma concluded that the high frequency area of this virus indicates that high density remains of Jōmon people.
Contributions to other populations Historical groups Full genome analyses of
Okhotsk culture remains on
Sakhalin show their descent from three major ancestral sources, notably
Ancient Northeast Asians,
Ancient Paleo-Siberians, and Jōmon people of Japan. An admixture analysis revealed them to carry c. 54% Ancient Northeast Asian, c. 22% Ancient Paleo-Siberian, and c. 24% Jōmon ancestries respectively. Jōmon ancestry is detected in other Far East Siberian individuals such as the 7,000-year-old Letuchaya Mysh individual and an outlier from the Middle Neolithic Boisman population (c. 29.7% ± 9.8%). Genetic analyses on ancient remains from the southern
Korean Peninsula during the
Three Kingdoms period reveal elevated Jōmon ancestry at c. 37%, while
Yayoi remains in Japan were found to carry nearly equal amounts of Jōmon ancestry (35–60%) and
Ancient Northeast Asian-like ancestry (40–65%). These results suggest the presence of the Jōmon people and their culture or a Jōmon-like population on the Korean peninsula and their significant contribution to the formation of early
Japonic-speakers. As such, the "agricultural transition in prehistoric Japan involved the process of assimilation, rather than replacement, with almost equal genetic contributions from the indigenous Jōmon and mainland Asian migrants of the Mumun/Yayoi period". The Jōmon-like ancestry in Korea was 'diluted' during the Late Neolithic to Bronze Age periods due to arrivals of
West Liao River farmer-related groups from Northeastern China. An analysis of some individuals from Northwestern Kyushu showed that some Yayoi-era individuals had 100% Jōmon ancestry, implying that admixture between Jōmon peoples and continental East Asian migrants was gradual. and shows the closest genetic affinities with the Late Jōmon individual from Shikoku, which was also similarly observed for Southern Ryukyuan Jōmon. Several ancient Northeast Asian individuals from inland East Asia (
Yumin) and the
Devil's Gate Cave (NEO240) can also be modeled as mixtures of deep lineages that are ancestral to the Jōmon and Tianyuan respectively, despite NEO240 being more related to the Jōmon. Yamamoto et al. 2024 found a wide range of Jōmon ancestry within different Japanese subgroups, ranging from 10–32%. Jōmon-related ancestry is also present in several Siberian (particularly in the
Ulchi at 7% and
Nivkh at 10%) and Southeast Asian groups. == In popular culture ==