Haplogroup D-M55 (M64.1/Page44.1) also known as Haplogroup D1a2a is a Y-chromosome haplogroup. It is one of two branches of Haplogroup D1a. The other is D1a1, which is found with high frequency in Tibetans and other Tibeto-Burmese populations and geographical close groups. D is also distributed with low to medium frequency in Central Asia, East Asia, and Mainland Southeast Asia.

Haplogroup D-M55 is found in about 33%^{[4][5][6][7][8]} of present-day Japanese males. It has been found in fourteen of a sample of sixteen or 87.5% of a sample of Ainu males in one study published in 2004^[9] and in three of a sample of four or 75% of a sample of Ainu males in another study published in 2005 in which some individuals from the 2004 study may have been retested.^[5] It is currently the most common Y-DNA haplogroup in Japan if O1-F265 and O2-M122 (TMRCA approx. 30,000 ~ 35,000 ybp) are considered as separate haplogroups. Haplogroup D-M55 may have been born in Japan at any time between its MRCA with D-Y34637 (found in present-day Onge and Jarawas) about 45,000 years ago and the MRCA of all extant branches of D-M55 about 21,000 years ago.

In 2017 it was confirmed that the Japanese branch of haplogroup D-M55 is distinct and isolated from other branches of haplogroup D since about 50,000 years ago. The split in D1a may have occurred near the Tibetan Plateau.^[10]

Among the subgroups of Haplogroup D, the ancestor of D-M55 went eastward to reach the Japanese archipelago.^[11] According to Michael F. Hammer of the University of Arizona, haplogroup D originated near the Tibetan Plateau and migrated into Japan were it eventually became D-M55.^[12] Mitsuru Sakitani said that Haplogroup D1 came from Tibet to northern Kyushu via the Altai Mountains and the Korean Peninsula more than, and Haplogroup D-M55 (D1a2a) was born in the Japanese archipelago.^[11]

Recent studies suggest that D-M55 became dominant during the late Jōmon period, shortly before the arrival of the Yayoi, suggesting a population boom and bust.^[13]

The average frequency in Japanese is about 33%.^[4][5][7][8] High frequencies are found in various places in Japan, especially in Hokkaidō, eastern Honshū, southern Kyūshū, and Okinawa.

• Ainu people: 87.5%（Tajima et al. 2004^[9]）
• Asahikawa (Hokkaido): 63.7% (estimated from Y-STR haplotypes)^[7]
• Chiba: 45.5%^[14]
• Tokyo: 40.4% (21/57 = 36.8% JPT, 23/52 = 44.2%^[14])
• Okinawa: 37.6% (0/7 Hateruma,^[15] 1/20 = 5.0% Iriomote,^[15] 8/29 = 27.6% Katsuren,^[15] 10/32 = 31.3% Yomitan,^[15] 16/49 = 32.7% Ishigaki,^[16] 13/38 = 34.2% Miyako,^[16] 13/36 = 36.1% Haebaru,^[16] 7/19 = 36.8% Gushikami,^[15] 35/87 = 40.2% Okinawa estimated from Y-STR haplotypes,^[7] 38/80 = 47.5% Itoman,^[15] 25/45 = 55.6% Okinawa^[5])
• Kanto region: 37.6%^[4]
• Kyushu: 35.0% (8/31 = 25.8% Fukuoka Prefecture,^[17] 29/104 = 27.9% Kyushu,^[9] 90/300 = 30.0% Nagasaki college students,^[8] 39/129 = 30.2% Saga Prefectural Chienkan Senior High School students,^[16] 34/102 = 33.3% Fukuoka adult men,^[8] 7/21 = 33.3% Nagasaki Prefecture,^[17] 13/37 = 35.1% Ōita Prefecture,^[17] 95/270 = 35.2% Miyazaki Prefecture,^[18] 470/1285 = 36.6% Miyazaki Prefecture,^[17] 58/151 = 38.4% Kagoshima Prefecture,^[17] 5/11 = 45.5% Saga Prefecture,^[17] 22/47 = 46.8% Kumamoto Prefecture^[17])
• Nagoya: 34.3% (estimated from Y-STR haplotypes)^[7]
• Sapporo: 33.9% (100/302 = 33.1% Sapporo college students,^[8] 72/206 = 35.0% Sapporo adult men^[8])
• Kawasaki: 33.0%^[8]
• Shizuoka: 32.8%^[5]
• Kanazawa: 32.6% (97/298 = 32.6%,^[8] 76/232 = 32.8%^[8])
• Aomori: 31.1% (22/79 = 27.8%,^[16] 11/27 = 40.7%^[5])
• Shikoku: 30% (18/70 = 25.7% Tokushima,^[5] 9/31 = 29.0% Shikoku,^[17] 119/388 = 30.7% Tokushima college students^[8]）
• Micronesia: 1/17 = 5.9％（Hammer et al. 2006^[5]）
• South Korea: 3/75 = 4.0% (Hammer et al. 2006^[5]), 12/317 = 3.8% (estimated from Y-STR haplotypes),^[7] 8/506 = 1.6% (Kim et al. 2011^[19])
• West Timor: 1/497 = 0.2%（Tumonggor et al. 2014^[20]）

A Jōmon period man excavated from Funadomari remains (about 3,800 - 3,500 YBP) in Rebun Island in Hokkaido belongs to Haplogroup D1a2a2a(D-CTS220).^[21]

The analysis of an Jōmon sample (Ikawazu) and an ancient sample from the Tibetan Plateau (Chokhopani, Ch) found only partially shared ancestry, suggesting a positive genetic bottleneck regarding the spread of haplogroup D from an ancient population related to the Tibetan Chokhopani sample (and modern Tibeto-Burmese groups).^[22]

By ISOGG tree（Version: 14.151）.^[23]

• DE (YAP)
  • D (CTS3946)
    • D1 (M174/Page30, IMS-JST021355, Haplogroup D-M174)
      • D1a (CTS11577)　
        • D1a1 (F6251/Z27276)
          • D1a1a (M15)　Tibet
          • D1a1b (P99)　Tibet, Mongol, Central Asia
        • D1a2(Z3660)
          • D1a2a (M64.1/Page44.1, M55) 　 Japan(Yamato people、Ryukyuan people、Ainu people)
          • D1a2b (Y34637)　Andaman Islands（Onge people, Jarawa people）^[24][25]
      • D1b (L1378) 　 Philippines^[26]
    • D2 (A5580.2) 　Nigeria, African American, Saudi Arabia, Syria^[27][28]