Tibetan macaques (Macaca thibetana) are a threatened primate species endemic to China. The current taxonomy of the species is based on external morphological and anatomical variations. To further understand the intraspecific variation and relationships among populations, we analyzed 44 mitochondrial DNA control region sequences (475 bp fragment) from individuals across the species range. Results revealed 11 major haplotypes with a high nucleotide diversity (0.792), but nucleotide diversity within haplotype lineages was only 0.042. Neighbor-joining phylogenetic analyses indicated support for four distinct haplotype clades corresponding to regional groups consistent with the recognized subspecies M .t. thibetana, M. t. guizhonensis, M. t. huangshanensis and M. t. pullus. As a result of regional geographic variation and genetic differences, we recommend the four subspecies should be considered different management units for conservation efforts.