In 2019, Dr. Hiroshi Tanaka, a geneticist at the University of Tokyo, stumbled upon a discovery that would change Japan’s historical narrative forever.

The Japanese government had kept a 3,800-year-old skeleton from northern Hokkaido hidden for decades, refusing to allow any genetic analysis.

But Dr.Tanaka’s courageous decision to sequence its DNA would unveil a truth so powerful it would challenge everything Japan knew about its origins.

The skeleton belonged to the Ainu people, Japan’s indigenous population.

For centuries, the Ainu were portrayed as primitive barbarians by the government, and their origins were dismissed as mere folklore.

Scholars long debated their mysterious past—some claiming the Ainu were Siberian invaders, while others believed they were the original inhabitants of Japan, pushed northward by waves of invaders.

The truth, however, was buried deep within their DNA.

The results of Dr.Tanaka’s work not only uncovered the Ainu’s true roots but also revealed that Japan’s true ancestors were not the people who now hold power, but the very group dismissed as outsiders.

The journey to uncover this truth began in 1865 when British explorer Thomas Wright Blakeston encountered a group of Ainu in Hokkaido.

He described them as looking more similar to his fellow countrymen than to any of the East Asians he had encountered, noting their thick, wavy beards and deep-set eyes.

They appeared to be completely different from the typical Japanese people, raising suspicions about their origins.

The Ainu elders passed down stories about their ancestors living throughout Japan, from Hokkaido to as far south as Tokyo, only to be driven out by invaders from across the sea.

For over a century, these oral traditions were dismissed as primitive myths.

In 1991, Dr. Masako Yamada made a groundbreaking discovery while analyzing DNA from Ainu volunteers.

What she found was astonishing.

The Ainu carried mitochondrial DNA markers that were completely absent in 99% of other Japanese populations.

The implications were clear: the Ainu were a distinct group, genetically different from the rest of Japan.

However, the real shock came in 1998 when construction workers uncovered over 500 ancient skeletons dating back to the Jomon period (16,000 to 300 BC) in Nagano Prefecture.

Among these remains was a perfectly preserved woman who had died 9,000 years ago.

Dr.Kenichi Shinoda analyzed her DNA and found it nearly identical to modern Ainu samples, confirming that the Ainu were direct descendants of Japan’s original inhabitants.

As researchers continued to delve into the genetic history of Japan, they compared the DNA of the Ainu to that of modern Japanese populations.

They discovered that the average Japanese person from Tokyo carried only 12% Jomon ancestry, while people from the ancient capital of Kyoto had just 9%.

Even the emperor’s family carried only 7% of this genetic heritage.

This startling revelation proved that Japan’s ruling class was predominantly descended from invaders, while the Ainu, whom the Japanese government had long marginalized, were the true indigenous people of Japan.

The Jomon period, during which the Ainu’s ancestors thrived, was followed by a slow migration of the Yayoi people from the Korean Peninsula, around 300 BC.

These agricultural migrants brought rice farming to Japan, which had a profound impact on the population.

The Yayoi people’s genetic markers eventually replaced much of the indigenous Jomon DNA, particularly in the southern parts of Japan.

However, in the northern regions like Hokkaido, the Ainu’s genetic markers remained relatively unchanged, shielded by the cold climate and isolation.

In 2019, when Dr. Tanaka analyzed the ancient DNA from a sacred Ainu burial site, he confirmed what had long been suspected: the Ainu were not recent arrivals from Siberia, but the direct descendants of the first people to inhabit Japan.

The discovery revealed that the true origins of the Japanese people lay not in the homogeneous narratives of invaders and immigrants, but in the indigenous Ainu population, whose culture and bloodlines had survived for thousands of years.

The revelation was nothing short of revolutionary.

The Ainu, once marginalized and dismissed, were proven to be the original Japanese, while the people who had dominated the islands for centuries—including the emperor—were the invaders.

This finding not only shattered historical myths but also forced Japan to confront its dark history of cultural suppression, ethnic discrimination, and forced assimilation of the Ainu.

DNA, it seems, has the power to uncover truths that no textbook or chronicle could ever reveal.