The Pamir Plateau, about one third of which is located in the southwest of Xinjiang, China, has vulnerable and unstable ecosystems, attributed to over 4,000 m above sea level on average and the extremely cold and dry climate. Studies on diversity of species, especially animals in this special plateau mountainous area are very limited. Due to its strong adaptability to extreme environment, Cape hare, Lepus capensis distributed in the Pamirs is one of the ideal model organisms used for understanding the evolution of species and assessing the relationships between species and environment. However, the classification of the Cape hare remains unclear by the traditional morphological methods. Therefore, in this study, we will determine the taxonomic status of Cape hare in Xinjiang Pamirs using both morphological and molecular genetics methods. Two mitochondrial DNA (mtDNA) markers, control region (D-loop) and cytochrome b (Cyt b) will be employed to detect genetic diversity of Lepus capensis in Xinjiang Pamirs and to explore the impact of specific plateau environment on the demographic history of the Cape hare by population genetics. This study will not only provide a scientific basis for protecting genetic and species diversity of Xinjiang Pamirs but also play an important role for the maintenance and stabilization of local ecosystem.