The frequency of Y-chromosome haplotypes consisted of thirteen single nucleotide polymorphism alleles in Bouyei people was investigated using PCR-RFLP. And the polymorphism of mitochondrial DNA Region V was studied. Nine Y-chromosome haplotypes (H1, H4, H5, H6, H7, H8, H9, H11, H12) and two mtDNA alleles (9-bp deletion) were obtained in the samples. The frequency distribution of these haplotypes and mtDNA polymorphisms in Bouyei people were very similar to that in Daic speaking populations including Zhuang, Li, Dong, and Yao people from Jinxiu, indicating a close genetic relationship among those populations implicating a common ancestry. A hypothesis of the origin of Bouyei people was proposed.