Yak (Bos grunniens) is a unique livestock animal originating from the Qinghai-Tibet Plateau in China. In the current study, we investigated the maternal genetic diversity, differentiation and phylogeny of wild yak population and four domestic yak breeds (Qinghai-Gaoyuan, Huanhu, Xueduo, and Yushu) in Qinghai, China by analyzing 166 mitochondrial cytochrome b (Cytb) gene sequence variations. Our results indicated that the haplotype and nucleotide diversities of wild yak were 0.883±0.044 and 0.004±0.002, while the total haplotype and nucleotide diversities of four Qinghai domestic yak breeds were 0.646±0.040 and 0.003±0.001, respectively. Among the four Qinghai domestic yak breeds, the haplotype diversity was found to be highest in Yushu yak breed (Hd = 0.770±0.053), while the lowest was recorded in Huanhu yak breed (Hd = 0.501±0.088). Estimates of FST values showed a moderate genetic differentiation between wild yak and Huanhu yak (FST = 0.058) as well as that between Huanhu yak and Yushu yak breeds (FST = 0.052), but a weak genetic differentiation was observed between the other yak breeds/populations (-0.021＜FST＜0.037). Additionally, the clustering analysis based on RST values showed that Xueduo yak and Huanhu yak were clustered into one group, and each of the other three yak breeds/populations was separated into one group, respectively. Overall, the clustering relationship between wild yak and Yushu yak was closer. Maternal phylogenetic analysis showed that wild yak and four local yak breeds/populations in Qinghai represented in three maternal lineages (Mt-Ⅰ, Mt-Ⅱ, and Mt-Ⅲ), indicating three maternal origins in yak. Our study would provide valuable information for the conservation and utilization of wild yak and Qinghai domestic yak breeds.