To investigate the molecular genetic diversity of wild yak (Bos grunniens mutus), the complete mitochondrial DNA D\|loop sequences of six wild yak bulls were cloned and sequenced (GenBank accession No.: FJ548840\|FJ548845). These sequences together with two D\|loop sequences of wild yak retrieved from the GenBank were aligned to determine the polymorphic loci and the number of haplotypes using software of BioEdit 7.0.9, DnaSP 4.10.1 and Arlequin 3.11. Moreover, the nucleotide diversity (π) and haplotype diversity (h) were calculated. The results showed that the lengths of mitochondrial DNA complete D\|loop sequences of the wild yak were between 891 bp and 894 bp, the average base contents of A, T, G and C were 32.68%, 28.65%, 13.46% and 25.21%, respectively, and the average content of A+T was up to 61.33%. There were 39 transitions or transversions (four insertion or deletion sites exclusive) including four single nucleotide mutation sites and 35 parsimony informative sites. According to the variation between the sequences, seven haplotypes were identified with h and π as of 0.9643 and 0.02144, respectively. These results indicated a considerable genetic diversity in the wild yak.