Three methods,CTAB-SDS-frozen-thawed,liquid nitrogen trituration and glass bead adsorptive process,were used to extract the metagenomic DNA of microbes in traditional fermented dairy products from Tibet,China.The results showed that modified CTAB-SDS-frozen-thawed can give a best extracting products,and the products can be used for further microbial diversity analysis.This research also analyzed the microbioal diversities of the samples using 16S rRNA-RFLP and ITS-PCR methods,the results showed that the samples of Longren township in Dangxiong province of Tibet expressed much more plenty microbial diversity,the dominant microbiology in these two samples also showed a high similarity.However,the microbiology in the samples of Namucuo township in Dangxiong province of Tibet showed a low abundance,and the dominant microbiology also expressed high difference with the samples of Longren township.The results illuminated that combined 16S rRNA-RFLP and ITS-PCR are powerful tool for estimating the community diversity of bacteria and true fungus in fermented dairy sample.