Within the genus Pseudois (Bovidae, Artiodactyla), two challenges are faced by taxonomists. First, the designation of the two subspecies of blue sheep, Pseudois nayaur nayaur and Pseudois nayaurszechuanensis, tends to be questionable with the accumulation of morphological and molecular data. Second, the taxonomic status of the dwarf blue sheep (Pseudois schaeferi) has been controversial since its discovery, and molecular analyses with relatively small sample sizes have not painted a clear picture. We collected samples and DNA sequence data from a broad geographic range in China to investigate the population structure of Pseudois nayaurszechuanensis and its phylogenetic relationship with Pseudois schaeferi. Employing mitochondrial cytochrome b and control region sequences, as well as the nuclear gene zona pellucida glycoprotein 3, further investigation was performed to extend upon previous studies. We found that the population of Helan Mountain of Ningxia Hui Autonomous Region has significantly differentiated from the populations in Qinghai, Gansu and Sichuan provinces, and may be classified as a new subspecies according to the 75% rule. The dwarf blue sheep was found to be some individuals of Pseudois nayaurszechuanensis with morphological variations and is not a species or subspecies, since they did not fall into a monophyletic group in the phylogenetic analyses with blue sheep. Gene flow between dwarf blue sheep and common blue sheep might have occurred in different areas of western Sichuan, which would result in the paraphyly of dwarf blue sheep.