Wild yak(Bos grunnients mutus), endemic Bovidae species in alpine region, is one of the most precious wild animal genetic resources in China. It has been listed as national protected animal. Our study analysed the whole sequence composition of mtDNA of wild yak and explored yak's taxonomic status. The results showed that the size of complete Mitochondrial genome of wild yak is 16 322 bp that include 22 tRNA genes, 2 rRNA genes, 13 protein coding genes and one D-loop region. The length of two rRNA genes, 22 tRNA genes, 13 code-length protein sequences and D-loop were 2528 bp, 1524 bp, 11420 bp and 892 bp respectively. The sequence has the characterization of no interval sequence, and the gene order is close with no intron. Wild yak have abundant genetic diversity.The phylogenetic trees constructed with whole mitochondrial genome sequences of wild yak, domestic yak, Zebu cattle, Cattle, Sheep, Chiru, Aoudad, Water buffalo, American bison, White rhinoceros, Greater Indian rhinoceros and Horse showed that the wild yak and domestic yak clustered firstly, and then meet with the American bison, followed with zebu/cattle and water buffalo.The yak is a species of the subfamily-Poephagus, and the domestic yak(Poephagus grunniens) and wild yak(Poephagus mutus) are two different species in the yak. The study has the great theoretical and practical significance for yak's origin, evolution and classification. At the same time, it is helpful to protection and utilization of wild yak genetic resources.