Japanese DNA
Genetic origins and closest populations · Japan · East Asia
Japan's population history is often described as a meeting of two main ancestries: the Jomon hunter-gatherers who lived on the islands for thousands of years, and rice farmers of the Yayoi period who arrived from the Asian mainland from about 3,000 years ago, with further continental input around the Kofun period according to recent ancient DNA work. In our model, the Japanese average is 71.0% East Asian, 22.6% Ancient Northeast Asian and 6.4% Southern Chinese Neolithic farmer. Our fixed set of sources has no Jomon reference, so that part of the story does not appear as a separate component here, and the fit (0.048) is only moderate. The closest ancient groups are Three Kingdoms-period Koreans from Daeseong-dong and Late Kofun people from Iwade in Japan, both at very close distances. The closest modern averages are Koreans, especially from Jeju Island, followed at a greater distance by Han Chinese from Shandong.
- Ancient components in our model: East Asian 71.0%, Ancient Northeast Asians 22.6%, Southern Chinese Neolithic farmers 6.4%
- Closest modern population in our data: Korean (Jeju Island), distance 0.0235
- Closest ancient group from Japan: Japan Iwade Late Kofun, distance 0.0242
Where does Japanese DNA sit on the genetic map of the world? To answer, we take the averaged Global25 (G25) coordinates of the Japanese individuals sampled in Japan and compare them with deep ancestral reference populations, with other modern groups and with ancient genomes. It is one of 335 populations in our atlas.
Ancient make-up of the Japanese average
Modelled as a mix of deep ancestral reference populations, the Japanese average comes out as 71.0% East Asian, 22.6% Ancient Northeast Asians and 6.4% Southern Chinese Neolithic farmers. The East Asian component reflects ancestry most common today in East Asia. With well over half of the total, this single source dominates the profile.
The fit is loose (fit distance 0.048), which usually means that none of the available reference populations is a close stand-in for part of this ancestry, so read the percentages as rough. This population was modelled with a global set of reference populations (ancient genomes, plus modern stand-ins where no suitable ancient genome exists), because West Eurasian sources alone cannot describe it.
Fenghuang – Sinosphere Report
Closest modern populations to Japanese
Genetically, the Japanese average sits nearest to Korean (Jeju Island) at 0.024, Korean at 0.033 and Korean (Yanbian Antu) at 0.036. On our scale, a distance of 0.024 counts as very close. By the tenth closest (Han (Shandong Weifang)) the distance grows to 0.054, a common pattern for a population that shares ancestry with its neighbours while keeping a profile of its own.
| # | Population | Distance | Closeness |
|---|---|---|---|
| 1 | Korean (Jeju Island) | 0.0235 | Very close |
| 2 | Korean | 0.0332 | Close |
| 3 | Korean (Yanbian Antu) | 0.0358 | Close |
| 4 | Han (Shandong Binzhou) | 0.0506 | Moderate |
| 5 | Baima | 0.0509 | Moderate |
| 6 | Han (Shanxi Shuozhou) | 0.0524 | Moderate |
| 7 | Manchu (Yhyegjl) | 0.0527 | Moderate |
| 8 | Manchu (Wusu) | 0.0528 | Moderate |
| 9 | Manchu | 0.0530 | Moderate |
| 10 | Han (Shandong Weifang) | 0.0536 | Moderate |
Distances are Euclidean distances between averaged G25 coordinates. On our scale, below 0.025 is very close, below 0.050 close, below 0.080 moderate, and beyond that distant.
Closest ancient populations to Japanese
Among ancient genomes, the closest match to the modern Japanese average is Korea Three Kingdoms Daeseong-dong (Three Kingdoms period, c. 57 BC-668 AD), at 0.020, followed by Japan Iwade Late Kofun and Korea Three Kingdoms Dangbuk-ri. That is a very close match, which suggests strong genetic continuity between those ancient people (or close relatives of theirs) and the modern population. A close ancient match is not proof of direct descent: it means those individuals carried a similar overall mix of ancestry.
| # | Ancient sample or group | Period | Distance |
|---|---|---|---|
| 1 | Korea Three Kingdoms Daeseong-dong | Three Kingdoms period, c. 57 BC-668 AD | 0.0200 |
| 2 | Japan Iwade Late Kofun | Kofun period, c. 250-540 AD | 0.0242 |
| 3 | Korea Three Kingdoms Dangbuk-ri | Three Kingdoms period, c. 57 BC-668 AD | 0.0275 |
| 4 | Korea Three Kingdoms Yuha-ri | Three Kingdoms period, c. 57 BC-668 AD | 0.0300 |
| 5 | China Shandong N Early-Middle Dawenkou Beiqian | Neolithic | 0.0359 |
| 6 | China Shandong N Longshan Wutai | Neolithic | 0.0365 |
| 7 | China Jiangsu N Middle Dawenkou Liulin | Neolithic | 0.0416 |
| 8 | Japan Ryukyu Early Modern Nagabaka | Early Modern, c. 1500-1800 AD | 0.0423 |
| 9 | China Shandong N Late Dawenkou Fujia | Neolithic | 0.0424 |
| 10 | China Shandong N Late Dawenkou Wucun | Neolithic | 0.0429 |
Ancient DNA from Japan
Our ancient DNA database holds 177 individuals excavated in present-day Japan, dated from about 17,950 BC to 1808 AD. The most frequent Y-DNA haplogroups among them are D1a (10), O1b (3) and B (1), and the most frequent mtDNA haplogroups are N9 (75), M7 (29) and G1 (16). These are people who lived on the same land in the past, not necessarily ancestors of today's Japanese population.
Most frequent Y-DNA haplogroups
Most frequent mtDNA haplogroups
| Haplogroup | Individuals | Examples |
|---|---|---|
| N9 | 75 | JpKa6904 Iyai1 Iyai4 |
| M7 | 29 | Higa006 Higashimyo JpOd274 |
| G1 | 16 | UsuMoshiriL-17a UsuMoshiriL-17c UsuMoshiriN-G5-208 |
| Y1 | 14 | HMN-1 HMN-10 HMN-13 |
| D4 | 13 | KitaKogane9 Irie12 Funadomari10 |
| A | 3 | FND-1 HMN-15 OMS-5 |
| B5 | 2 | JpIw32 FND-2 |
| C3 | 2 | HMN-12 HMN-2 |
Ancient DNA studies on Japan
- Female-biased continental farmer ancestry contribution to the modern Japanese genome (2026)
- Population expansion of early Upper Palaeolithic hunter-gatherers triggered cultural complexity on Paleo-Honshu Island, Japan (2026)
- Ancient Ryukyu Jomon contributed to past and current genetic structure of Japanese populations (2026)
- Ancient genomes reveal early-stage admixture and genetic diversity in the Northwestern Kyushu Yayoi (2026)
- Towards On-Site Paleogenomics: Application and Perspective of Nanopore Sequencing with Ancient DNA (2025)
- Genome of an early Okhotsk individual reveals ancient admixture between Jomon and Kamchatka lineages (2025)
- Ancient Genomes Reveal Early-Stage Admixture and Genetic Diversity in the Northwestern Kyushu Yayoi (2025)
- Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations (2024)
Browse them in our ancient DNA database: 177 from Japan.
Compare yourself with Japanese
Paste your G25 coordinates (scaled, one line, with or without a name in front) and we compute your genetic distance to the Japanese average and to its closest neighbours, right in your browser. Nothing is uploaded or stored.
| # | Population | Your distance | Closeness |
|---|
This list only covers Japanese and its neighbours. To find out which of our reports actually fits your DNA, run the free Report Finder: it runs the same fit test that every report uses before an order.
No G25 coordinates yet? Get a free simulated G25 from your raw DNA file, or order G25 coordinates.
About these numbers
Keep in mind that a population average is a statistical summary of a limited number of sampled individuals. Real people inside any group vary, some carry more of one ancestry and some less, and no genetic profile decides who is or is not Japanese. Use these numbers as a map of deep ancestry, not as a label.
Method: averaged G25 coordinates, Euclidean distances to other modern and ancient averages, and a non-negative least-squares model against deep ancestral reference populations (data generated 2026-10-01). Read the full method.
Go deeper than the average
This page describes the Japanese average. Your own DNA has its own story: Fenghuang – Sinosphere Report (15€) models your genome against the ancient sources and modern communities of the region, era by era, in a personal PDF report.
A report built for people of Sinosphere / East Asian ancestry: ancient regional core (Yellow & Yangtze River Neolithic, Erlitou/Shang/Zhou dynasties, Han Dynasty, Yayoi migration, Tang Dynasty, Manchu/Qing era) versus non-regional outside...
More populations from East Asia
Frequently asked questions
What is the ancient genetic make-up of Japanese?
Modelled with deep ancestral reference populations, the Japanese average is about 71.0% East Asian, 22.6% Ancient Northeast Asians and 6.4% Southern Chinese Neolithic farmers. These proportions are model estimates for a group average, not exact values for any one person.
Which populations are genetically closest to Japanese?
In the G25 data, the closest modern populations to the Japanese average are Korean (Jeju Island), Korean and Korean (Yanbian Antu). The closest ancient matches are Korea Three Kingdoms Daeseong-dong, Japan Iwade Late Kofun and Korea Three Kingdoms Dangbuk-ri.
Can a DNA test tell me if I am Japanese?
No DNA test can confirm an ethnicity or a nationality. What DNA can show is how similar your genome is to the sampled Japanese average and to its neighbours. If you have G25 coordinates, paste them in the comparison box on this page to check that for free.
Which ExploreYourDNA report suits Japanese ancestry?
For the Japanese average, the regional report to choose is Fenghuang – Sinosphere Report, which our fit test rates as a good match. Your own DNA may differ from the average, so the free Report Finder checks every report against your file before you buy.
Where does the data on this page come from?
From the averaged Global25 (G25) coordinates of the sampled individuals: genetic distances to other modern and ancient population averages, and a non-negative least-squares model against deep ancestral reference populations. The full method is described at https://www.exploreyourdna.com/populations#method.