Abstract MtDNA D-loop sequences and cranial morphometrics were used to analyze the phylogenetic relationships of bharal (Pseudois nayaur szechuanensis) populations. The habitat preferences of bharal were also investigated in Helanshan, Ningxia. The results from the analysis of mtDNA D-loop sequences and cranial morphometrics were in accordance. Among all populations analyzed, the phylogenetic relationships between populations in Lixian, Sichuan and Helanshan, Ningxia were most distantly related, while populations in Dulan, Qinghai and Subei, Gansu were close to one another. No matter in summer or winter, bharal generally prefer to stay in meadows, but they would appear in forests and shrubs as well.