The rhesus macaque (Macaca mulatta) is perhaps the most widely distributed nonhuman primate, is used more extensively than any other primate species as animal models for the study of biomedicine. In this study, we sequenced and analysed a fragment of 491 bp of mitochondrial DNA (mtDNA) partial control region in 230 individuals belonging to 8 populations of Sichuan province of China. Among the 230 individuals, we observed 56 different haplotypes defined by 110 polymorphic sites. The average number of nucleotide differences (k) was 18.844, indicating that very high genetic differentiation and the extant Sichuan wild rhesus macaques population consists of diverse genetic groups in their maternal lineage. The mtDNA haplotypes of these Sichuan wild rhesus macaques clustered into two main clades (CladeⅠand Clade Ⅱ), may correspond to M. m. vestitus and M.m.lasiotis.