# Jōmon people

Jōmon people (縄文 人, Jōmon jin) is the generic name of the indigenous hunter-gatherer population that lived in the Japanese archipelago during the Jōmon period (c. 14,000 to 300 BC). They were united through a common Jōmon culture, which reached a considerable degree of sedentism and cultural complexity.
The Jōmon people are characterized by a deeply diverged East Asian ancestry and contributed around 10–20% ancestry to modern Japanese people. Population genomic data from multiple Jōmon period remains suggest that they diverged from "Ancestral East Asians" prior to the divergence of Northern and Southern East Asians, sometime between 38,000 and 25,000 years ago, but after the divergence of "Basal East Asian" Tianyuan and Hoabinhian lineages (c. 39,000 years ago). After their migration into the Japanese archipelago, they became largely isolated from outside geneflow at c. 20,000 to 25,000 BC although there is evidence of influence from northern and southern East Eurasian groups.

## Etymology

Jōmon (縄文, Jōmon), sometimes written as Jomon (American English /ˈdʒoʊˌmɑːn/ JOH-mahn, British English /ˈdʒəʊmɒn/ JOH-mon), literally meaning "cord-marked" or "cord pattern," is a Japanese word coined by American zoologist, archaeologist, and orientalist Edward S. Morse in his book Shell Mounds of Omori (1879) which he wrote after he discovered sherds of cord-marked pottery in 1877 at the Ōmori Shell Mound dating to the period now known as the Jōmon period. He subsequently translated "straw-rope pattern" from English to Japanese as Jōmon to refer to the people living during this period of Japanese history. Other names for jomon pottery have been used in the first few decades after the discovery such as “Ainu school pottery” and “Shell mound pottery” before the term jomon was widely accepted by the archeological community. It’s only in 1937 that the historian Yamanouchi Sugao used the pottery term to define the pre-rice agriculture period related to this same pottery.
The word is composed of two kanji: 縄 and 文.
* 縄 (jō) using its Go-on reading, means "rope" or "cord," specifically "a flexible, heavy cord of tightly intertwined hemp or other fibers." This kanji derives etymologically from Old Japanese, from the Proto-Japonic napa, related to the verb 綯う (nau, "to plait or twist together into twine or line").
* 文 (mon), also using its Go-on reading, here means "design" or "pattern." Etymologically, this meaning originates from Middle Chinese 文 (mjun, "ornate; a kind of coin; language, literature, letter, character"). In modern Japanese, the kanji 紋 (mon) is more frequently used to explicitly represent "pattern" or "design" which is composed of the radicals 糸 (ito, thread) and 文 (mon).
It can be used as a common noun meaning "cord pattern," or as a proper noun which is the short version referring specifically to the Jōmon period. These kanji appear in various related terms, creating a lexical field centered around Jōmon culture, including:
* 縄文時代 (Jōmon jidai, "Jōmon period")
* 縄文式土器 (Jōmon-shiki doki, "Jōmon ware")
* 縄文人 (Jōmon-jin, "Jōmon people")
* 縄文土器 (Jōmon doki, "Jōmon pottery")

## History of Jōmon Archeology
### Early descriptions and depictions

The study of the Jōmon people and their material culture has evolved significantly since the Edo period. One of the earliest recorded depictions of Jōmon artifacts dates back to Edo-period antiquarians, who sketched and documented unusual pottery sherds found in shell middens. The 18th-century traveler Sugae Masumi mentioned Jōmon-era remains in his writings, including his book Sumika no Yama (c. 1800), which referenced shell mounds and prehistoric pottery discovered during his travels. Early antiquarians often misidentified these remains as relics of legendary figures or lost civilizations rather than indigenous Japanese prehistory.
During the early Meiji period (1868-1912), the emergence of modern archaeology in Japan led to a more systematic study of prehistoric remains. The first significant scholarly recognition of Jōmon culture came in 1877, when Edward S. Morse, an American zoologist and orientalist, excavated the Ōmori Shell Mound near Tokyo. Morse coined the term Jōmon (縄文, “cord-marked”) to describe the distinctive pottery he uncovered, characterized by impressions made using twisted cords. His work marked the beginning of formal archaeological study of the Jōmon period, although early interpretations remained influenced by Western models of cultural evolution.

### Early 20th-century theories and discoveries

By the early 20th century, Japanese archaeologists began conducting their own excavations, shifting from foreign-led expeditions to national research initiatives. Scholars such as Tsuboi Shōgorō and Torii Ryūzō further investigated shell middens, burial sites, and Jōmon settlements. Kokugaku (National Learning) scholars sought to frame Jōmon culture within Japan’s historical narrative, often contrasting it with later Yayoi-period rice agriculture. During the 1920s-30s, Kojima Gizaemon and Hamada Kōsaku led efforts to establish regional typologies of Jōmon pottery, classifying styles into chronological phases based on stratigraphy. Excavations at sites such as Kasori Shell Midden (Chiba) provided crucial evidence of long-term settlement and subsistence patterns. However, pre-war interpretations of Jōmon society were heavily influenced by Western diffusionist theories, with many scholars viewing Jōmon culture as primitive and stagnant compared to “more advanced” agricultural societies.
The post-World War II era saw a major shift in Japanese archaeology, fueled by the rapid expansion of academic institutions and government-funded excavations. Researchers such as Serizawa Chōsuke and Yamanouchi Sugao played key roles in redefining Jōmon chronology, refining pottery typologies, and identifying major Jōmon sub-periods (Incipient, Initial, Early, Middle, Late, Final).

### Post-war expansion and new interpretations (1945-1990s)

Between the 1950s and 1970s, archaeology in Japan expanded rapidly due to post-war reconstruction projects and large-scale public works. The Cultural Properties Protection Law (1950) required archaeological investigations before construction, leading to the excavation of thousands of Jōmon sites. The discovery of large settlements, such as Sannai Maruyama (Aomori) in the 1990s, revealed that Jōmon groups lived in permanent or semi-permanent villages, contradicting earlier assumptions that they were exclusively nomadic hunter-gatherers.
By the late 20th century, new perspectives emerged regarding Jōmon social complexity. “Complex hunter-gatherers” theory became widely accepted, recognizing Jōmon societies as displaying features typically associated with agricultural civilizations, such as long-term settlement, social hierarchy, and advanced craft specialization (e.g., lacquerware, jade ornaments, figurines). International collaboration also increased, with researchers drawing comparisons between Jōmon society and other prehistoric cultures, such as the North American Pacific Northwest and Mesolithic Europe.

### 21st-century advances and theoretical shifts

The 21st century has seen major advancements in Jōmon archaeology, driven by scientific dating techniques, DNA analysis, and interdisciplinary studies.
* Chronological Refinements: Advances in radiocarbon dating (AMS C-14 dating) have refined the Jōmon timeline, pushing back the origins of pottery to 16,500 BCE at sites like Ōdai Yamamoto I (Aomori). This supports the idea that Japan was one of the earliest centers of pottery production in the world.
* Ancient DNA Analysis: Genetic studies of Jōmon skeletal remains (e.g., from Funadomari Shell Midden) have provided insights into their genetic baggage and legacy.
* Environmental Adaptation Studies: Climate reconstructions suggest that Jōmon societies adapted to Holocene climate fluctuations, moving between coastal and inland settlements as sea levels changed.
* Jōmon Ritual and Symbolism: Research into ceremonial sites, such as Ōyu Stone Circles (Akita) and Omori Katsuyama Stone Circle (Aomori), indicates that Jōmon people constructed monumental ritual landscapes, challenging earlier perceptions that only agricultural societies built large-scale structures.
* UNESCO Recognition: In 2021, 17 Jōmon sites across Hokkaidō and northern Honshū were inscribed as UNESCO World Heritage sites, recognizing Jōmon culture as one of the longest-lasting forager traditions in the world.

## Lifestyle

The culture of the Jōmon people was largely based on food collection and hunting, but it is also suggested that the Jōmon people practiced early agriculture. They gathered tree nuts and shellfish, were involved in hunting and fishing, and also practiced some degree of agriculture, such as the cultivation of the adzuki bean and soybean. The Jōmon people also used pottery, and generally lived in pit dwellings.

### Settlements

Settlements changed throughout the Jōmon period and its different phases.
* Incipient Jōmon settlements were the first sedentary settlements in Japan, had no facilities, and only consisted of dwellings. An example of such a settlement is the Odai Yamamoto 1 Site.
* Initial Jōmon settlements developed their first facility: the grave site. The residential area and the cemetery were separated. An example of such settlement is the Kakinoshima site.
* Early Jōmon settlements gained more facilities: the storage area and the dump area. Sites representative of this period are the Kitakogane site, Tagoyano site, and Futatsumori Site.
* Middle Jōmon saw the apparition of hub settlements and the division of dump and ritual spaces. Sites representative of this period are the Sannai-Maruyama Site, Ōfune Site, and Goshono site.
* Late Jōmon see the dissolution of hub settlements into smaller ones with a shared ritual center between them into which was incorporated a cemetery. Some of the sites of this period include the Irie site, Komakino Site, Isedōtai Ruins, and Ōyu Stone Circles.
* Final Jōmon sees the separation of the ritual site and the cemetery into 2 different but still multi-settlement shared sites. Some of the sites in this category are: Kiusu Earthwork Burial Circles, Ōmori Katsuyama Site, Takasago Burial Site, Kamegaoka Stone Age Site, and Korekawa Site.
Dug out roads have been excavated in Sannai Maruyama, which linked the multiple facilities of the settlement and served for the transport of goods and people through the settlement and to other smaller settlements. On both sides of the roads were aligned graves. Other facilities excavated include pit dwellings, large pit dwellings, dumping grounds, mounds, pit graves, children graves, graves with stone circles, storage pits, regular and large pillar-supported structures, and watering place for soaking Japanese horse chestnuts.
Pit dwellings are buildings built by digging a shallow hole in the ground and installing a roof over it, with a hearth in its center. As they are relatively small on average, it is thought that families of 4 to 6 people spanning 2 to 3 generations lived in each dwelling. The roofs were made of bark or thatch and may have been covered with soil. Altars may have been installed in some of them.
Pit dwellings longer than 10m are considered large pit dwellings and were most likely community spaces such as a meeting venue, a community workshop or a winter residence.

### Tools

The Jōmon people used obsidian, jade and different kinds of wood for their crafting.
Stone tools were used, mainly chipped stone tools, made of siliceous shale, but also obsidian, and other stones. Those types of tools included but were not limited to: spearheads, arrowheads, scrapers (tanged, stemmed, or not), semi-circular flat chipped stone tools (which are believed to have been used to prepare plant foods), knives, and stone drills.
Other stone implements made without the chipping process included ground stone axes (made from granodiorite, greenstone, or blueschist), abrasion cutting stone tools, whetstones, grinding stones (with or without pit), hammer stones, saddle querns, and stone weights.
Antlers and bones were also used for toolmaking such as for spatulas, fish hooks, harpoon heads, drills, and needles. Exclusive to antlers were hammers, using the base of the antler as the impact surface.
Wood was used for shafts of spears, arrows, and harpoons, and for bows and digging sticks while strips of bark were used to weave baskets.
Tools with shafts such as spears and arrows had their heads secured using bitumen.

### Hunting

The Jōmon people were skilled hunter capable of targeting a variety of preys. Among them were:
* Flying Squirrel
* Hare
* Weasel
* Fox
* Squirrel
* Raccoon Dog
* Wild Boar
* Deer
* Bear
* Sea Lion
* Badger
* Ape
* Otter
* Marten
* Cormorant
* Albatross
* Pheasant
* Grebe
* Geese
* Duck
The percentages of prey of each species vary from site to site but generally, wild boars and deer were at the center of the meat diet of the Jōmon. However, in the Sannai Maruyama site, flying squirrels and hares are the dominant sources of meat most likely due to environmental factors.
Hunting techniques included bows, arrows, spears, pitfall traps, and hunting dogs.

### Fishing

There is evidence that the Jōmon people built ships out of large trees and used them for fishing and traveling; however, there is no agreement as to whether they used sails or paddles.
Many species of fishes and seafood were excavated in dumping grounds. These species lived in a variety of different habitats leading to the conclusion that the Jōmon had a vast knowledge of the sea.
Some of the fish species found are:
* Yellowtail amberjack
* Right-eyed Flounder
* Shark
* Mackerel
* Herring
* Flounder
* Scorpion fish
* Globefish
* Fat Greenling
* Pacific Sea bream
* Pacific cod
Fishing techniques used were harpoons, fishing spears, line fishing, and nets. Harpoon heads were detachable and had a hole at their base to tie a rope through it and reel the prey. Harpoons and spears were used to fish larger preys. Line fishing was done with antler or bone fish hooks. Two types of fish hooks existed: single-ended and coupled (or combined). Coupled fish hooks had barbs while single-ended did not but both had notches to tie the line. Stone weights were attached to nets to act as sinkers.
Shellfishes were also gathered including Japanese oysters, Ezo abalones, clams, crabs, octopuses, squids, mantis shrimps, and other crustaceans.

### Plant gathering

The Jōmon grew trees in areas near their settlements and gathered edible plants. The most commonly consumed plant was the chestnut. The tree was also used as fuel and building materials.
Other plants that were part of the diet include walnut, Japanese horse chestnuts, adzuki bean, Udo, silver vine, elderberry, wild grape, mulberry, raspberry, and yam. Digging sticks were used to dig up yam.

### Food processing

It is possible that the Jōmon might have been able to process elderberries into alcohol. Nuts, walnuts, and chestnuts were collected during autumn and were kept in storage pits or indoor inside large earthenware pots. Before use, they were crushed with hammer stones or grinding stone on top of saddle querns. Japanese horse chestnut and other chestnuts with strong scents were soaked in water to mellow the taste.
At the Sannai Maruyama site, a watering place was discovered that may have been used to process nuts through soaking. The remains were a reservoir of water that was filled and emptied by the stream's spring.

### Cooking

Cooking was done on the fireplace of the dwelling using smaller earthenware pots than the ones used for storage.
During the Middle Jōmon period, earthenware was made in various shapes including pedestal shallow shapes, dishes, and bowls; all thought to have been used to serve food.
Round bottom wooden containers are thought to have been held in one hand while pouring liquids.

### Trade networks

Jōmon people had extensive trade networks spanning hundreds of kilometers. Primary traded materials included obsidian, gemstone (such as jade), amber, asphalt, stone used for ground stone axes (granodiorite, greenstone, blueschist), and red pigments.
Some materials were sent raw to other sites while others were processed into finished products first before being traded. Some sites also specialized in the trade of certain raw materials or processed goods. For example, the Sannai Maruyama site, a trading hub, specialized in the refining of jade into goods but had to trade pre-made obsidian tools from Hokkaido and Nagano, with this latest being around 700 km from Sannai Maruyama.
The trade of goods between Hokkaido and Honshu indicates that the Jōmon were good navigators and some experts theorize that trade was mostly conducted in dugout canoes on the coastlines.
According to a 2006 study, it is likely that the Jōmon traded with southern Chinese and Southeast Asians via Fujian.

## Culture

Some elements of modern Japanese culture may have come from the Jōmon culture. Among these elements are the precursory beliefs to modern Shinto, some marriage customs, some architectural styles, and possibly some technological developments such as lacquerware.

### Pottery

The style of pottery created by the Jōmon people is identifiable for its "cord-marked" patterns. The pottery styles characteristic of the first phases of Jōmon culture used decoration created by impressing cords into the surface of wet clay, and are generally accepted to be among the oldest forms of pottery in East Asia and the world. Next to clay pots and vessels, the Jōmon also made many highly stylized statues (dogū) and clay masks.

### Lacquerware

Lacquerware included wooden bowls, dishes, and combs. It was mixed with red pigments to give it a red color. Lacquer tree sap was collected from cultivated and managed areas. The steps to make lacquerware were:
* Collect the sap
* Remove the excess moisture
* Purify the sap
* Mix it with red pigments
* Apply the lacquer by hand to the ware
Red pigments were made from ferrous quartz, then ground into powder before mixing it with lacquer. Some pottery was directly painted with red pigments instead of lacquering it.

### Clothings

Fabric made with twisted warp called angin were found at Sannai Maruyama. It is believed that cloth and clothings were made of weaved twisted plant fiber such as hemp in this way.
The Jōmon people also practiced sewing using bone and antlers needles.

### Jewelry and accessories

A wide variety of materials were used for accessories such as clay, stone, bone, shells, and lacquered wood. Ornaments may have been used both for special occasions and for everyday life.
Hair ornaments including hairpins made of bones, and combs made of lacquered wood were excavated. They are thought to have been used to decorate hairs after they were tied up.
Cylindrical or drum-shaped clay earspools were put into a pierced earlobe, while slit-stone earings were put through it.
Pendants made of stone, including precious stones such as jade, and clay have been found with perced holes in them, a thread was passed through them to attach them to one's neck or to the waist. Some pendants were made of clay. Magatama were likely invented by one of the Jōmon tribes, and are commonly found throughout Japan and less in Northeast Asia.
Some ornaments were made from animal parts such as bear canine tooth or wild boar tusk. Jade is thought to have been worn for special occasions such as festivals and rituals.

## Religion

It is suggested that the religion of the Jōmon people was similar to early Shinto (specifically Ko-Shintō). It was largely based on animism, and possibly shamanism. Other similar religions are the Ryukyuan and Ainu religions. Certain strange stone implements in various shapes are thought to have been used as talisman.

### Rituals and festivals

Accessories and jewelry are thought to have been worn more during special occasions such as festivals, burials, and rituals than in everyday life.
Central ritual sites outside settlements and belonging to multiple villages have started to appear during the Late Jōmon period but hub settlements also acting as central ritual hubs appeared during the Middle Jōmon period.
Mounds were built using refuse from soil excavation and daily life activities but were not merely dumping grounds, instead they had special significance as places of rituals.
Stone and clay figurines are believed to have been used for festivals. Many represented women with breasts and parts or holes possibly representing genitalia. They are thought to have been a way of praying for fertility in festivals. Asphalt has been used on some of them to attempt to repair them.
Miniature pottery are earthenware in extremely small sized modeled after utilitarian-sized vessels such as deep bowls for cooking and storing and shallow bowls for serving food. They are thought to have been used in ceremonies rather than as toys due to their excavations in ceremonial mounds.
Other objects found in ceremonial mounds include triangular pottery (theorized to be simplified versions of clay figurines), stick-shaped clay objects (thought to be a miniature pottery version of stone rods), stamp-shaped stones (thought to be modeled after female genitalia), walnut clay objects (created by pressing clay against inner shell of walnuts), and pottery with human figure (theorized to be shamans with head ornaments and tools).
Sword-shaped artifacts made of whale bone have been excavated and are though to have been used in fire related rituals as most have burned marks. The Jōmon also crafted stone batons or rods and swords which are thought to have been used for rituals and festivals as many have been exposed to fire. Other artifacts such as large jade beads have also been exposed to fire.
In Sannai Maruyama, a large structure made of 6 great pillars of chestnuts between 1 and 2 meters in diameter has been repeatedly built through the ages. It is thought to have played multiple roles such as a ritual venue, totem pole, observatory, lighthouse, and watchtower.

### Burials

Graves were different for different people with adult graves being different from children's and from a few important people.
* Adults were buried in pit graves, some with pebbles acting as grave markers or soil mounds on top of them.
* Important people were buried in pit graves surrounded by stone circles.
* Children were buried in reused everyday pottery and placed together away from the other graves: some had modifications done to the pottery such as breaking the rim or piercing holes at the bottom or side of it. It is possible that only infant were buried in this fashion. Some of them had fist-sized circular pebbles or flaking tools in them.
Most graves did not contain grave goods. For those that had them, it is believed that men and women were buried with different objects: hunting tools and stone arrowheads, and cooking utensils such as saddle quern respectively.
In Sannai Maruyama, pit graves have been excavated on both sides of roads, feet towards the road at slight angles. At this same site, pillar-supported structures may have been used for temporary resting place for the deceased.

## Languages

It is not known what language or languages were spoken in Japan during the Jōmon period. Suggested languages are: the Ainu language, Japonic languages, Austronesian languages, or unknown and today extinct languages. While the most supported view is to equate the Ainu language with the Jōmon language, this view is not uncontroversial or easily acceptable as there were probably multiple distinct language families spoken by the Jōmon period population of the Japanese archipelago.
Alexander Vovin (1993) argues that the Ainu languages originated in Central Honshu, and were later pushed northwards into Hokkaido, where the early Ainu-speakers merged with local groups, forming the historical Ainu ethnicity. Bilingualism between Ainu and Japanese was common in Tohoku until the 10th century. According to Vovin (2021) there is also some evidence for the presence of Austronesian languages close to the Japanese archipelago, which may have contributed some loanwords to early Japanese.
Some linguists suggest that the Japonic languages may have been already present within the Japanese archipelago and coastal Korea, before the Yayoi period, and can be linked to one of the Jōmon populations of southwestern Japan, rather than the later Yayoi or Kofun period rice-agriculturalists. Japonic-speakers then expanded during the Yayoi period, by assimilating the newcomers, adopting rice growing, and fusing mainland Asian technologies with local traditions.

## Origins

The Jōmon people represent the descendants of the Paleolithic inhabitants of the Japanese archipelago, which became isolated from other mainland Asian groups some 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 and 38,000 years ago, before the divergence of Ancient Northern East Asians and Ancient Southern East Asians, but after the divergence of the Upper Paleolithic Tianyuan lineage and ancient Southeast Asian hunter-gatherer lineage (Hoabinhians). Like other East Asian populations, the ancestors of the Jōmon people originated from Southeast Asia and expanded to East Asia via a coastal route. They represent one of the "earliest waves of migration".
The Jōmon lineage displays a closer genetic affinity to Ancient Northern and Southern East Asian lineages, compared to Basal East Asian Tianyuan or Hoabinhian lineages, and have a similar divergence date as the "Longlin" ancestry from ancient Guangxi. Beyond their genetic affinity with other Eastern Asian lineages, the Jōmon also display a weak genetic affinity with the Yana Rhinoceros Horn Site specimen, associated with Ancient North Eurasians (or Ancient North Siberians), which may point to geneflow between both groups prior to their isolation from other East Eurasian populations. According to Bennet et al. 2024, "one explanation may be that Tianyuan-like early ancestors of the Jōmon interacted with groups that entered Siberia through a northern migration route". This geneflow may be associated with the introduction of microblade technology to northern Japan, yet no support for direct geneflow from ANE-like (MA-1) sources into the Jōmon could be found, suggesting instead a non-demic diffusion. Genetic affinities with lowland East Asians and northeast Siberians, may further indicate later contact episodes between the Jōmon and other East Eurasian populations.
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 if spending too much time in the sun. However, according to a 2016 study, the derived allele of the EDAR gene is found in 25% of Ainu. Also, there are high frequencies of variants of the OCA2 gene and ADH gene cluster among Ainu, which are widespread in East Asia but virtually absent elsewhere.
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, inline with the inferred admixture among modern Japanese peoples. Watanabe et al. (2023) 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. However, Yamamoto et al. (2024) stated that the association of Jomon ancestry with the decrease of height is observable only if principal components are not accounted for in the test, indicating that this association can be confounded by population stratification. They also found indications for an influence on the Body Mass Index, including a higher risk of obesity among modern Japanese, but also higher frequency of "active functions in skeletal muscle cells" and "increased bone mineral density", which may have been related to the hunter-gatherer lifestyle of the Jōmon people.
Studies show that populations from Tohoku, Kanto and Kyushu were more genetically related to Ryukyuan populations whilst populations from Kinki and Shikoku were more related to continental East Asian populations. There are also stronger genetic affinities between Ainu and mainland Japanese in western Hokkaido. Liu et al. (2024) states that Jōmon ancestry was the highest in southern Japan, especially Okinawa (28.5%), followed by northeastern Japan (19%) and western Japan (12%).

#### Haplogroups

It is thought that the haplogroups D-M55 (D1a2a) and C1a1 were frequent among the historical Jōmon period people of Japan. O-M119 is also suggested to have been presented in at least some Jōmon period remains. 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, albeit with much lower frequency, in Koreans. 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. Haplogroup C1a1 has been found regularly in about 6% of modern Japanese. Elsewhere, it has been observed sporadically in individuals from South Korea, North Korea (South Hwanghae Province), and China (ethnic Korean in Ning'an and Han Chinese in Linghai, Guancheng Hui District, Haigang District, and Dinghai District). 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.
The MtDNA haplogroup diversity of the Jōmon people is characterized by the presence of haplogroups M7a and N9b.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 Jomons while M7a is found frequently among the Honshu Jomons. However N9b is found only at very low percentage among the Honshu Jomon. M7a is estimated to share a most recent common ancestor with M7b'c, a clade whose members are found mainly in Japan (including Jōmon people), other parts of East Asia, and Southeast Asia, 33,500 (95% CI 26,300 <-> 42,000) years before present. All extant members of haplogroup M7a are estimated to share a most recent common ancestor 20,500 (95% CI 14,700 <-> 27,800) years before present. Haplogroup M7a now has its highest frequency in Okinawa.
A 2018 study states that Okhotsk‐type and Siberian-type haplogroups significantly contributed to the genetic makeup of Edo-era Ainu, along with mainland Japanese, contrary to the popular belief that Ainu received little genetic input from mainland Japanese before the Meiji-era colonization of Hokkaido.
According to a 2022 study, haplogroup M7a was found in both northern and southern sites in Early Jōmon Japan, 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 Funadomari whilst D4b2 and D4h2 were common in the Shomyoji shell midden and Funadomari respectively. In the Final Jomon, N9b prevailed in Hokkaido whilst 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.

### Morphological characteristics

Several studies of numerous Jōmon skeletal remains that were excavated from various locations in the Japanese archipelago allowed researchers to learn more about the Jōmon period population of Japan. The Jōmon people were relatively close to other East Asian people, however shared more similarities with Native American samples. Within Japan, regional variance among different Jōmon remains was detected. Historically, the Jōmon people were classified as Mongoloid.
Skeletal and dental features of different Jōmon groups were found "to resemble either Southeast Asians, Upper Paleolithic Asians, or Northeastern Asians, as well as present-day indigenous populations of the Ainu of Hokkaido and Ryukyu Islanders", although they were adapted to their hunter-gather lifestyles and to an extent, their cold climates.
Dental morphology suggests that the Jōmon had Sundadont dental structure which is more common among modern Southeast Asians and indigenous Taiwanese, and 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.
Kondo et al. 2017, analyzed the regional morphological and craniometric characteristics of the Jōmon period 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-Jomon crania being mesocephalic and Okinawan crania being brachycephalic. They concluded that the "Jomon 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 Jomon population seemed to proceed in eastern or central Japan, not western Japan (Okinawa or Kyushu regions); (b) the Kyushu Jomon could have a small-sized and isolated population history; and (c) the population history of Hokkaido Jomon 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 genetic, or phylogenetic, and environmental effects. But Gakuhari et al. 2020 clarifies that Hokkaido and Honshu Jōmon cluster together and form a clade to the exclusion of other groups.
According to Chatters et al., the Jōmon display some similarities to the Native American Kennewick Man. Chatters, citing anthropologist C. Loring Brace, classified Jōmon and Polynesians as a single craniofacial "Jōmon -Pacific" cluster. Chatters, citing Powell, argues 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". Powell further elaborates that dental analysis showed the Jōmon to be of the Sundadont type. According to Matsumura et al. (2019), the Jōmon were phenotypically Australo-Papuan, similar to prehistoric populations from southern China and Southeast Asia. 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 still closer related to later East Asians despite phenotypic discontinuities, pointing to a legacy of Paleolithic variations lost in modern Eastern Asian populations. A 2021 study states that these populations also resemble modern Sri Lankan Veddahs, Aboriginal Australians and Papuans and Africans, reflective of their direct Out of Africa origin.
Craniofacial features of the Jōmon people were significantly retained by the Ainu and Okinawans/Ryukyuans. The former 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. The latter 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 Takuo 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.
The path of natural infection of this virus is limited to vertical infection between women and children (most often through breastfeeding) and horizontal infection between males and females (most often from males to females through sexual intercourse).
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 found them to be derived from three major 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.
Genetic analyses on ancient remains from the southern Korean Peninsula revealed 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 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 Jomon" and mainland Asian migrants of the Mumun/Yayoi period.

#### Modern groups

Jōmon-associated ancestry is commonly found throughout the Japanese archipelago, ranging from c. 15% among modern Japanese people, to c. 30% among Ryukyuan people, and up to c. 75% among modern Ainu people, and at lower frequency among surrounding groups, such as the Nivkhs or Ulch people, but also Koreans and other coastal groups, suggesting that the Jōmon were not completely isolated from other groups. Wang and Wang (2022) noted that peoples with Jōmon ancestry during the Three Kingdoms period significantly contributed to the genetic makeup of modern Koreans. But this ancestry was 'diluted' over time due to subsequent arrivals of Neolithic West Liao River farmers from northeast China.
McColl et al. (2018) states that present Southeast Asians derive ancestry from at least 4 ancient population sources. One source was the mainland Hòabìnhians, who shared ancestry with the ancient Japanese Ikawazu Jōmon, along with present-day Andamanese Önge and Malaysian Jehai. However, according to Yang et al. (2020), the Jōmon individual showed affinities to several coastal Neolithic populations in Siberia and southern East Asia, with the latter clustering with present-day southern East Asians.
Along with modern Japanese, Ulch, and Nivkhs, present-day Taiwanese aborigines (i.e. Ami and Atayal) also showed excess allele sharing with a 2,500 year old individual in mainland Japan, which was characterized by 'typical Jōmon culture'.

## In popular culture

Aspects of the Jōmon culture and pottery were used in the video game The Legend of Zelda: Breath of the Wild. Nintendo's art director Takizawa Satoru said that the Jōmon culture was the inspiration for the "Sheikah slates, shrines and other ancient objects" in the game.
A recreated Jōmon village in the form of an experience park (Sarashina no Sato), which offers different activities, can be visited in Chikuma, Nagano.