Abstract: Eleven cores from DK-2 gas hydrate borehole in Qilian Mountain permafrost, located in the north of the Tibetan Plateau, were investigated to find out the difference between gas hydrate samples and non-gas hydrate samples by microbial community analysis. Of all the genes often found in marine gas hydrate samples, i.e., bacterial and archaeal 16S rDNA, mcrA(Ⅰ,Ⅱ), pmoA, mmoX and mxaF, bacterial 16S rDNA could be observed in all of the eleven samples, resulting in the detection of a great quantity of bacterial sequences belonging to 5 phylums, i.e., Proteobacteria, Actinobacteria, Bactemides, Firmicutes, and Deinococcus-Thermus. The bacteria diversity decreases with the increasing depth. A study of gas hydrate sample DK2-19 and non-gas hydrate sample DK2-25 selected for phylogenetie analysis and diversity comparison shows that the two samples are remarkably different from each other. A comparison between gas hydrate samples and non-gas hydrate samples show that the percentage of γ-Proteobacteria in gas hydrate samples is lower than that in non-gas hydrate samples, and Arthrobacter could be found mainly in non-gas hydrate samples.