Pseudois nayaur had been listed as an endangered wild animal by the International Union for Conservation of Nature. It is belonging to the second grade national protected animal in China. In recent years, human activities including logging, hunting, road building and overgrazing of pastures had caused significant decrease of P. nayaur population. Understanding the genetic diversity status and the population structure in different geographic population of P. nayaur would contribute to the development of systematic conservation strategies. A total of 226 faece samples were obtained from Jinsha River Valley and 169 sequences of control region belonging to 4 haplotypes were amplified. The population of the P. nayaur showed a relatively high haplotype diversity but low levels of nucleotide diversity (h=0.68, pi=0.0242). We concluded that the P. nayaur population of Jinsha River Valley had a very low genetic diversity. The phylogenetic tree constructed based on maximum parsimony method suggested that the four geographical populations in Jinsha River valley were clustered into two subclades of Pseudois nayaur szechuanensis. At the same time, all samples of dwarf P. nayaur from Batang county and the partial P. nayaur from Quzonggong sampling station were found to share the same haplotype. The molecular clock analysis suggested that the dwarf P. nayaur and the P. nayaur were diverged from 0.39 Mya to 0.32 Mya. It appeared that the evolutionary history of P. nayaur, such as divergences and population dispersal might be strongly affected by climate fluctuation in the early mid-Pleistocene (1.05~0.36 Mya). Based on the migration ability of P. nayaur, we suggested that from Baima Mountain Nature Reserve to Zhubalong Nature Reserve along Jingsha River Valley should be conserved as integrated habitat for these populations.