To date, the genetic structure and genetic diversity of Lepus capensis in Xinjiang has not been systematically studied at the molecular level, and its subspecies taxonomic status has been under debate for years. According to traditional morphology, there are three subspecies of L. capensis distributed in Xinjiang: L.c. centrasiaticus, L.c. lehmanni and L.c. pamirensis. In this study, we determined 592 bp D-loop sequences of 87 cape hares from Xinjiang Province. Forty-four haplotypes were defined based on 148 polymorphic sites. Both the haplotype diversity (0.977+/-0.005) and nucleotide diversity (0.064+/-0.031) are high. FST P values are significantly high and no haplotype was shared among the four geographic populations, indicating that genetic differentiation among populations is significant. AMOVA shows that most of the genetic differentiation occurred among geographic groups, indicating that geographic isolation such as mountains and deserts might make an effective barrier against gene flow. Both the phylogenetic tree and median-joining network grouped 44 haplotypes into four distinct clades corresponding to four geographic areas, indicating an obvious phylogeographic pattern. Our data supported the subspecies status of L. c. lehmanni. The fact that haplotypes of L. c. centrasiaticus were grouped into two distinct clades suggests that this traditional subspecies should be considered as two subspecies. In addition, L. c. pamirensis shows a significantly higher sequence divergence compared to other subspecies, and the difference even reached the level of species.