To investigate the genetic diversity, clustering relationship, genetic differentiation and classification, we presented molecular variation analysis of partial mitochondrial(mt) DNA D-loop from 296 individuals encompassing 10 yak breeds. The aligned 637 bp fragments included 61 variable sites, and a total of 77 haplotypes were identified. The genetic diversity analysis demonstrated that there was significant difference between breeds of domestic yaks. Among 10 yak breeds, Huanhu yak and Bazhou yak showed the highest and the lowest haplotype diverisity (0.9848±0.0403 and 0.8000±00825), respectively. Where as for the nucleotide diversity, Sibu yak and Bazhou yak presented the highest and the lowest values (0.022582±0.011767 and 0.006856±0.002476), respectively. In all domestic yaks, a high genetic diversity was observed with 0.9251±0.0095 for haplotype diversity and 0.015265±0.007757 for nucleotide diversity. The clustering relationship indicated that 10 yak breeds could be divided into two clades. The first clade included only Sibu yak, and the second clade consisted of the remaining 9 breeds. The result showed that there is no significant correlation between genetic distance and geographic distribution in yak breeds. Analysis of molecular variance (AMOVA) revealed remarkably significant genetic differentiation (ΦCT=0.05285, P<0.01) between Jiulong-Sibu-Jiali group and multi-breeds group. However, no significant genetic differentiation was detected among breeds within groups (ΦSC= 0.00648, P>0.05). These data suggested that 10 yak breeds should be classified into two types. Our result accorded with previous study conducted by Professor Caili, and provided direct genetic evidence for reasonable classification of domestic yak breeds.