Microbes inhabiting the desert respond sensitively to environmental changes and may be an indicator for changes in the desert ecosystem. Hypolithic microbial communities in the desert play a vital role in ecosystem processes such as soil for-mation and organic matter accumulation. This study investigated and compared the culturable bacterial community struc-ture and diversity in hypolithic and peripheral soils, and the interaction between bacteria and environmental factors. The bacteria were isolated using four different kinds of media and identified by 16S rRNA gene-sequence analysis. The num-bers of culturable bacteria in the hypolithic and peripheral soils ranged from 3.0×104 to 3.6×105 CFU/g and from 6.5×104 to 5.3×105 CFU/g, respectively, indicating that the bacteria number in peripheral soil was higher than that in hypolithic soil. A total of 98 species belonging to 34 genera were identified, among which Arthrobacter, Bacillus, and Streptomyces were found dominantly and widely distributed. The community of culturable bacteria had obvious sample specificity, and the diversity in hypolithic soil was higher than that in peripheral soil. On the regional scale, the distribution of culturable bacteria and the environmental factors showed regular changes. On the local scale, the high heterogeneity of the hypolithic environment determined the specificity of the number and species of culturable bacteria.