Abstract: This study aimed to explore the composition and diversity of microorganisms in raw milk of yak and cattle-yak. The 16S rDNA V4 region of those two kinds of raw milk was sequencing by high-throughput technology and comparative analysis of bioinformatics.The results showed that a total of 5516 OTUs were obtained with 97% similarity level.The comparison of microbial phylum levels shows that Proteobacteria, Firmicutes and Actinobacteria were the common dominant bacteria phylum for yak milk and cattle-yak milk.The relative abundances of the three Microbes in the yak milk were 29.80%, 35.99% and 8.41%, respectively. The relative abundances of the three microbes in the cattle-yakmilk were 45.36%, 25.79% and 7.39%, respectively. At the genus level, the dominant genus of yak milk was unidentified-Cyanobacteria, and the relative abundance was 9.32%. The dominant genus of cattle-yak milk was Bradyrhizobium, which accounts for 11.53%. At the species level, Bradyrhizobium elkanii and Kosakonia oryzae were the dominant strains in milk of yak and cattle-yak. The two strains accounted for 2.42% and 3.36% in yak milk, respectively.And the two types of bacteria account for 11.53% and 5.53% of the milk in the cattle-yak, respectively. Alpha diversity analysis shows that there are significant differences between different milk richness estimates (P<0.05).And the richness and diversity ofcattle-yak milk was higher.