The distribution of the first PC suggested a possible single origin of all the Kra–Dai populations. The second PC indicated a deep division of the Kra–Dai peoples into two: east group and west group. The center of the east group is in Zhejiang, China, and that of the west one is on the border between China and Burma. The third PC implies the migration routes southern China towards northeast, northwest and southwest during the relocation of Kra–Dai populations. The gene flow between Kra–Dai and populations of other ethnic groups are noticeable. Han Chinese in Zhejiang and Shanghai have the highest concentration of Kra–Dai types of Y haplotypes among all the Han populations in China, suggesting a possible expansion of Kra–Dai peoples from southern China to Zhejiang via Jiangxi. Kra–Dai in Zhejiang and Fujian might have come by different routes, as suggested by the difference of their profiles. A diphyletic genetic structure was found in Taiwan Aborigines. The West Kra–Dai, Tai, Thai, Ahom and so on emigrated from southern China rather late. It might have happened one to two thousand years ago.