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The Ainu people of Japan is notable for possessing almost exclusively Haplogroup D chromosomes

In human genetics, Haplogroup D (M174) is a Y-chromosome haplogroup.

D is believed to have originated in Africa some 50,000 years before present. Along with haplogroup E, D contains the distinctive YAP polymorphism, which indicates their common ancestry.

Both D and E also contain the M168 change, which is present in all Y-chromosome haplogroups except A and B.

Like haplogroup C, D is believed to represent a great coastal migration along southern Asia, from Arabia to Southeast Asia and thence northward to populate East Asia. It is found today at high frequency among populations in Tibet, the Japanese archipelago, and the Andaman Islands, though curiously not in India. The Ainu of Japan and the Jarawa and Onge of the Andaman Islands are notable for possessing almost exclusively Haplogroup D chromosomes, although Haplogroup C chromosomes also occur among the Ainu at a frequency of approximately 10%, similar to the Japanese. Haplogroup D chromosomes are also found at low to moderate frequencies among all the populations of Central and Northeast Asia as well as the Han and Miao-Yao peoples of China and among several minority populations of Yunnan that speak Tibeto-Burman languages and reside in close proximity to the Tibetans.

Unlike haplogroup C, it did not travel from Asia to the New World.

Haplogroup D is also remarkable for its rather extreme geographic differentiation, with a distinct subset of Haplogroup D chromosomes being found exclusively in each of the populations that contains a large percentage of individuals whose Y-chromosomes belong to Haplogroup D: Haplogroup D1 among the Tibetans (as well as among the mainland East Asian populations that display very low frequencies of Haplogroup D Y-chromosomes), Haplogroup D2 among the various populations of the Japanese Archipelago, Haplogroup D3 among the inhabitants of Tajikistan and other parts of mountainous southern Central Asia, and Haplogroup D* (probably another monophyletic branch of Haplogroup D) among the Andaman Islanders. Another type (or types) of Haplogroup D* is found at a very low frequency among the Turkic and Mongolic populations of Central Asia. This apparently ancient diversification of Haplogroup D suggests that it may perhaps be better characterized as a "super-haplogroup" or "macro-haplogroup."

The Haplogroup D Y-chromosomes that are found among populations of the Japanese Archipelago are particularly distinctive, bearing a complex of at least five individual mutations along an internal branch of the Haplogroup D phylogeny, thus distinguishing them clearly from the Haplogroup D chromosomes that are found among the Tibetans and Andaman Islanders and providing evidence that Y-chromosome Haplogroup D2 was the modal haplogroup in the ancestral population that developed the prehistoric Jōmon culture in the Japanese islands.

The subclades of Haplogroup D with their defining mutation, according to the 2006 ISOGG tree:

• D (M174)
  • D*
  • D1 (M15) Typical of the Tibetans
  • D2 (M55, M57, M64.1, M179, P12, P37.1, P41.1 (M359.1), 12f2.2) Typical of the Ainu, Ryukyuans, and Japanese
    • D2*
    • D2a (M116.1)
      • D2a*
      • D2a1 (M125)
        • D2a1*
        • D2a1a (P42)
        • D2a1b (P53.2)
      • D2a2 (M151)
  • D3 (P47) Occurs at a moderately high frequency among populations of southern Central Asia

• Spread of Haplogroup D, from National Geographic