To understand the patrilineal genetic structure of Baiyue ethnic group in Guizhou province, we studied the frequencies of Y-chromosome haplotypes which consisted of 10 single nucleotide polymorphisms (SNPs) by using the PCR-RFLP method. Five haplotypes were found in Baiyue ethnic group in Guizhou, among which H8 was the most common, whereas that of Miao in Guizhou tended to be H8, H11 and H12 haplotypes. Compared with Miao in Guizhou, the Guizhou Baiyue (excluding Sui and Dong) was significantly different and could be regarded as an independent ethnic group. Differences were also found in the same ethnic group among different areas.