The Super Science High School (SSH) consortium, in which high schools from various regions (Yaeyama Islands, Miyako Island, Okinawa Main Island, Saga Prefecture, Hyogo Prefecture, Miyagi Prefecture, and Aomori Prefecture) participate, have analyzed different Y-chromosomal and mitochondrial DNA (mtDNA) haplogroups from 2008 to 2012. In this study, we investigated the distribution of haplogroups in the above-mentioned areas. For Y chromosome, haplogroups DE*, and C1 showed higher frequency in the Ryukyu area (Yaeyama Islands, Miyako Island, and Okinawa Main Island) than in the Saga and Aomori Prefectures. However, haplogroup C3 showed lower frequency in the Ryukyu area than in Saga and Aomori Prefectures. Haplogroup O2b1 showed lower frequency in Okinawa Island, whereas haplogroups O2b* and O3 did not show any marked variability across regions. For mtDNA, haplogroups M7a and N9a showed higher and lower frequencies, respectively, in the Ryukyu area than in the Saga, Hyogo, and Aomori Prefectures. However, haplogroup N9b showed lower frequency in the Hyogo, Osaka, Kyoto, and Saga Prefectures than in the Ryukyu area and Aomori Prefecture. In conclusion, there seems to be a significant difference in the distribution of Y chromosomal and mtDNA haplogroups between mainland Japan and the Ryukyu area.