The distribution of Y-chromosome SNP haplotypes in 30 Kra–Dai populations were studied. Among the 19 SNPs studied, M119, M110, M95, and M88 are most informative in delineating the genetic structure of Kra–Dai. Linguistic and cultural classification are in general concordance with the genetic classification, although it may be transgressed due to the apparent gene flow between the major branches of Kra–Dai. For example, some populations of the Kadai, a major branch of Kra–Dai, are more similar to the populations of the Kam–Sui, another major branch. This phenomenon may be the result of the unitary self-identification and geographic assimilation of Kra–Dai system. The geographic distribution of the three principal components (PCs) were generated by superimposing the loading coefficients of each population onto a map, respectively.