In this study, the microbial diversity of metagenomics in naturally fermented yak milk(kurut) were investigated using barcoded pyrosequencing. A total of 3051 unique V3 variable regions of the 16S rRNA gene of bacterium and 3396 unique ITS variable regions of fungi were analyzed from two kurut samples. The results indicated that the abundance of fungi was higher than bacteria in the kurut samples. The Firmicutes and Ascomycota were the most abundant bacteria and fungi phyla in kurut samples. At genus levels, the bacteria of kurut were largely composed of the Lactobacillus while Galactomyces was the dominant genus within the fungus of kurut.