DNAtestJōmon, Yayoi and Kofun: The Three Ancestries of the Japanese
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For decades, textbooks said the Japanese descend from two peoples: the ancient Jōmon hunter-gatherers and the Yayoi rice farmers who arrived from the Korean peninsula. In 2021, ancient DNA showed that story was missing a piece. There were three.
In short
- Jōmon hunter-gatherers lived across Japan for more than 10,000 years and made some of the world's earliest pottery.
- Yayoi rice farmers crossed from the Korean peninsula from about 900 BCE and mixed with the Jōmon.
- A third wave in the Kofun period (c. 300–710 CE) brought new East Asian ancestry that now makes up the largest share of most mainland Japanese people's DNA.
- Jōmon ancestry survives most strongly among the Ainu of Hokkaido and in the Ryukyu Islands.
1. The Jōmon: 10,000 years of hunters, fishers and potters
From about 14,000 BCE, the Jōmon lived across the whole Japanese archipelago, from Hokkaido to the Ryukyu Islands. They fished, gathered shellfish, hunted deer and boar, and tended chestnut groves. Unusually for hunter-gatherers, many lived in permanent villages. Sannai-Maruyama in northern Japan was home to hundreds of people over 1,500 years, with pit houses and a towering structure built on chestnut-tree pillars.
The Jōmon were among the first people on Earth to make pottery. Their name means "cord-marked," after the patterns they pressed into clay. Over time their pots grew into the wildly ornate "flame-style" vessels of the Middle Jōmon. They also made clay dogū figurines, whose purpose is still a mystery.
What DNA revealed: the Jōmon were a deeply distinct population. Their ancestors split from other East Asians many thousands of years before the end of the last Ice Age, then lived in relative isolation on the islands.
2. The Yayoi: rice, bronze and a new way of life
From about 900 BCE, people crossing from the Korean peninsula began settling in northern Kyushu. They brought irrigated wet-rice farming, bronze and iron tools, and weaving. (Radiocarbon dating pushed this arrival centuries earlier than the traditional date of 300 BCE.)
Farming villages spread east across Honshu and grew into fortified settlements. Yoshinogari in Kyushu had moats, watchtowers and hundreds of buildings. Communities cast bronze dōtaku bells for rituals likely tied to the harvest. By the 3rd century CE, Chinese chronicles describe the land of Wa and its shaman queen, Himiko, who sent envoys to China.
How they blended: the Yayoi didn't replace the Jōmon. Ancient genomes show the two groups mixed, and the Jōmon way of life lasted longest at the edges of the archipelago, in the far north and the far south.
3. The Kofun: the ancestry nobody expected
The Kofun period is named for its tombs. Japan's rulers were buried under enormous keyhole-shaped mounds ringed with clay haniwa figures of warriors, horses and houses. The largest, the Daisen Kofun near Osaka, is about 486 meters long, one of the biggest burial monuments ever built.
It was also an age of newcomers. Immigrants from the Korean kingdoms and China, known in Japanese history as toraijin, brought Chinese writing, Buddhism, advanced ironworking, horse riding and new pottery techniques. Many served the rising Yamato court, the state from which Japan's imperial line claims descent.
What DNA revealed: in 2021, researchers sequenced ancient genomes from across Japanese prehistory. Kofun-period people carried a large new wave of East Asian ancestry that earlier Japanese people lacked. That overturned the two-source model. This Kofun-era ancestry makes up the largest share of most mainland Japanese people's DNA today.
How the three ancestries mix today
| Ancestry | Arrived | Strongest today in |
|---|---|---|
| Jōmon | Before 14,000 BCE | The Ainu of Hokkaido and the Ryukyu Islands (Okinawa); a smaller share of mainland Japanese DNA |
| Yayoi (Northeast Asian) | From about 900 BCE | A part of most Japanese people's DNA |
| Kofun (East Asian) | About 300–700 CE | The largest share for most mainland Japanese |
Japan is a striking example of a pattern ancient DNA keeps finding around the world: a population that looks uniform today is really a blend of several waves of people who arrived at different times and mixed.
Can a DNA test show Jōmon ancestry?
Not directly. The ethnicity estimates from AncestryDNA, 23andMe and MyHeritage compare you with people living today, so they'll report something like "Japanese" or "Korean," not "Jōmon." To separate the three ancient layers, your DNA has to be compared with ancient genomes, which is what we're building.
One clue you can check today is your haplogroup. Paternal haplogroup D-M55 (labeled D1a2a or D1b, depending on the version of the tree) is strongly associated with the Jōmon, and maternal haplogroups such as N9b and M7a are also linked to Jōmon ancestry. 23andMe reports haplogroups, and FamilyTreeDNA offers the deepest tests.
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Try the free analyzerFrequently asked questions
Are the Japanese descended from the Jōmon?
Partly. Most Japanese people carry some Jōmon ancestry, but it's a minority of their DNA. It's much higher among the Ainu and in the Ryukyu Islands.
Where did the Yayoi come from?
From the Korean peninsula. Their ancestry is related to peoples of the Korean peninsula and northeast China.
Who are the Ainu?
The Ainu are an Indigenous people of Hokkaido, northern Honshu and formerly Sakhalin and the Kuril Islands. They carry the highest share of Jōmon ancestry of any living people.
Which DNA test is best for East Asian ancestry?
23andMe's database has good East Asian coverage and reports haplogroups. See our best DNA test picks for other options.