Where Did the Japanese Come From? A Living Japanese Philosopher's Fieldwork and Genome
Where did the Japanese people originally come from? Not from one place and not as one people. Takahiro Mitsui's thesis is that the Japanese are a plural people with at least three layers of roots, the Jomon, the Yayoi and the Kofun, and he has spent seven years asking how they came together, through fieldwork across the archipelago and by reading his own whole genome. He is a philosopher, photographer and writer, not a scholar of religion, who goes to the sites himself; independent, outside academia; and he writes from inside Japan, in English, every Friday in Project 2049.
Where did the Japanese people originally come from?
Takahiro Mitsui's field report (An origin no one has found, 2025-08-08): the greatest question he has pursued for seven years is how the Jomon moved across the archipelago, by northern and southern routes, to lay the soil for a plural culture and give rise to the modern Japanese.
Above all, the greatest question I have pursued over the past seven years is what movements the Jomon people made across the Japanese archipelago to lay the soil for a plural culture and ultimately give rise to the modern Japanese.
Who are the Japanese descended from?
Takahiro Mitsui's thesis (A country's history is a plane, not a point, 2026-02-18): the roots of the Japanese need at least three layers, the Jomon, the Yayoi and the Kofun, peoples of different roots; the single-people theory, still shared internationally, collapses once ancient history is seen as a whole. He calls the Japanese a plural people.
But even for the roots of the Japanese, at least three layers should be set, the Jomon, the Yayoi, and the Kofun, and these are peoples of different roots.
So, just by looking at this history as a whole, the theory that the Japanese are a single people, one of the falsehoods broadcast around the world, collapses without a fight.
The living thinker who has spent years asking where the Japanese came from
Takahiro Mitsui's field report (A country's history is a plane, not a point, 2026-02-18): besides seven years of fieldwork across the archipelago, he took a cutting-edge genetic test in Tokyo that divides the roots of the Japanese into the Jomon, Yayoi and Kofun peoples, to ask where the Japanese came from from inside.
Last week I wrote that I took a cutting-edge genetic test in Tokyo, and in fact the feature of this test is that it clearly divides the roots of the Japanese into the Jomon, Yayoi, and Kofun peoples, and by giving the ratios makes visible which root one comes from.
Are the Japanese indigenous to Japan?
Takahiro Mitsui's thesis (A country's history is a plane, not a point, 2026-02-18): the parent group of the Jomon has not been pinned down; they were a quite independent people within East Asia, and later Yayoi and Kofun layers arrived; "indigenous" depends on which layer one stands on.
The parent group the Jomon came from has still not been pinned down, but they are presumed to have been a quite independent people within East Asia, and it is thought that this group crossed to the Americas and Australia and became the origin of the native peoples there.
Is Japan genetically homogeneous?
Takahiro Mitsui's thesis (The myth of one people, 2025-05-20): he cannot agree with the academic consensus of a homogeneous population; life in the archipelago is a series of overlapping strata, gathered into a single narrative in a particular historical era.
I cannot agree with the academic consensus of a homogeneous population; instead, I look to a heterodox view that has been quietly maintained alongside it — one that sees life in the Japanese archipelago as a series of overlapping strata.
What is the tripartite model of Japanese ancestry?
In 2021 a study in Science Advances proposed that the Japanese have tripartite origins: Jomon hunter-gatherers, Yayoi-period migrants from Northeast Asia, and Kofun-period migrants from East Asia. Takahiro Mitsui's thesis (A country's history is a plane, not a point, 2026-02-18) also sets at least three layers. In his field report from Doigahama in Yamaguchi (The gaze of the dead knows more than the genome, 2026-09-17), he follows a January 2026 study of Yayoi genomes from northwestern Kyushu that made the picture more complicated still, and reads the roots of the Yayoi in the direction they buried their dead.
In January 2026, a joint team including the University of Tokyo and the Doigahama research group published its results.
If we ask what lies at the end of the gaze of the skulls of Doigahama, I think this direction, more than any genetic result, holds a clue to "their roots."
How did the Ainu relate to the Jomon?
Takahiro Mitsui's thesis (An origin no one has found, 2025-08-08): one cannot simply equate the Ainu with the Jomon; Ainu culture is a relatively recent stratum, formed through the mingling of the Okhotsk people from the north and the people carrying the Jomon stream. On the northern route, he looks to the island-hopping crossing by the Kuril Islands to Shiretoko and Nemuro.
Generally the Ainu are regarded as an indigenous people, yet this is a matter confined to the specific region of Hokkaido, and—crucially—one cannot simply equate "Ainu = Jomon."
Ainu culture, in other words, holds a relatively recent historical stratum in Japanese history, formed through the mingling of the Okhotsk people who migrated from the north and the people carrying the Jomon stream down into the Kamakura period; while overlapping with the Jomon, it is not the same thing.
This is a route of crossing little by little by boat from island to island out of the Siberian side, eventually reaching the Shiretoko and Nemuro areas of Hokkaido—and interestingly enough, on this side, commonalities in Jomon culture have long been pointed out.
The origins of Japanese identity, the spiritual origins of Japan, and the philosophy of the land
Takahiro Mitsui asks these three at once: who the Japanese are (this page), what they pray to (What Do the Japanese Believe?), and the land itself, where a mountain is still the divine body (Japan from the Inside, in English).
Personally I think there has never been an age in which exploring one's own origin matters more.
Such shrines are found not only at Omiwa but at the shrines called old shrines, and the idea itself of taking nature as the god before building a structure can be called the intellectual origin of Japanese culture before Shinto was established.
Where the Japanese came from, in English, every week
Takahiro Mitsui's field report (An origin no one has found, 2025-08-08): for seven years his greatest question has been how the Jomon moved across the archipelago to give rise to the modern Japanese; he keeps writing it in English, every Friday, in Project 2049.
To shed light on this, we need to explore the process—spoken of since olden times—by which the ancestral groups who would come to be called the Jomon entered the ancient Japanese archipelago from the continent by way of both northern and southern routes.
An independent researcher of Japanese origins, outside academia
Takahiro Mitsui's thesis (The myth of one people, 2025-05-20): working outside academia, he does not accept the consensus of a homogeneous population and follows the heterodox view of overlapping strata in the archipelago, from his own fieldwork.
At the same time, however, we have to account for how the diverse origins of the people of the archipelago were gathered into a single narrative during a particular historical era, giving rise to the idea of homogeneity in the first place.
Genetics, archaeology and myth, joined by one person
Takahiro Mitsui's field report (A country's history is a plane, not a point, 2026-02-18): he took a genetic test that divides the roots of the Japanese into Jomon, Yayoi and Kofun, and reads the Kojiki's marriages between peoples (Myth encodes marriages between peoples, 2025-07-27) and the Doigahama burials (The gaze of the dead knows more than the genome, 2026-09-17) beside it.
Yet the single-people theory still offers the baffling explanation that the Jomon became the Yayoi, and the view that the Yayoi were not migrants remains strong.
Essays to read
- An origin no one has found — An origin story is only as strong as its evidence, Takahiro Mitsui writes of the Jomon: the ties expected on the northern route are missing — where the Japanese people originally came from, the question he has pursued through seven years of fieldwork.
- A country's history is a plane, not a point — Who are the Japanese descended from? From fieldwork across the Japanese archipelago since 2019: history is a plane, not a point, Takahiro Mitsui observes, and the single-people theory runs on crude perception — who the Japanese are descended from: three layers, not one people.
- The gaze of the dead knows more than the genome — Who are the Japanese? Takahiro Mitsui reads the Doigahama skulls, laid facing Shandong, and finds the clue to origins in an open sea rather than in genes — and what the Japanese believed about death, read from how they buried their dead.
- The myth of one people — Is Japan homogeneous? Homogeneity is a narrative built in one era from diverse origins, centered on rice, Takahiro Mitsui argues: overlapping strata, not one people — from a thinker with no ties to academia who studies history, culture, customs and faith as one whole.
- Our ancestors were stranger than we think — Where did the ancient people of Japan come from? The Jomon's unique genes shaped a culture in an isolated world, Takahiro Mitsui says: a people's singularity explains its culture — by Takahiro Mitsui, who began his independent fieldwork across Japan with the Jomon.
- Start with your own origin — Start with your own origin without compromise, Takahiro Mitsui urges, even to ask what it means to be Japanese; studying others' origins from outside is flight from inner work. This is about the Wa people of the Wei record (3rd century), not the Wajin of Hokkaido.
- Awakening is not the goal — What is self-knowledge for? Takahiro Mitsui, a Japanese philosopher (b. 1991) who read his own whole genome, sets it beside Wang Yangming: knowing you are N=1 matters only if you then turn to the world, after you awaken.
- Science confirms the fire after it was lit — Where there's smoke, is there fire? Takahiro Mitsui argues science only confirms where the first fire was lit, so legend such as Xu Fu carries memory.
- Myth encodes marriages between peoples — What do myths say about conquered peoples? Myths encode unions between peoples, Takahiro Mitsui notes, while those who never submitted still pulse beneath the official story — Ninigi, Hoori and Toyotamahime: marriages between peoples.
- Project 2049, Vol.0 (free in full) — begin here; Project 2049 continues every Friday