[Objective] Lake sediments store huge amount of specific microorganisms that greatly contribute to biogeochemical processes in lake ecosystems. However, there is little information about the vertical distribution of microbial community along lake sediment profile. In this study, we investigated the abundance and structure of pristine sediment bacterial communities along a depth gradient (0?20 cm) in a freshwater lake Puma Yumco and a saline lake AWongco on the Tibetan Plateau. [Methods] Real-time quantitative PCR (qPCR) and denaturant gradient gel electrophoresis (DGGE) were used to determine the bacterial abundance and community structure, respectively. [Results] Bacterial abundance consistently decreased along vertical depth in the two lake sediments and the abundance decreased from 1012 to 1010 in freshwater lake and from 1011 to 108 in saline lake, respectively. Bacterial abundances in freshwater lake were one order of magnitude higher than those in saline lake at each vertical depth. DGGE analysis showed that the bacterial richness was significantly higher (p=0.014) in freshwater lake than saline lake sediments; the bacterial community composition was clearly different between these two lake sediments, and the communities differed between upper (0?7 cm) and lower (7?20 cm) depths. Phylogenetic analysis showed that Gamma-proteobacteria, Bacteroidetes, Deinococcus-Thermus and Cyanobacteria were present in saline sediments while Delta- and Beta-proteobactria, Acidobacteria and Chloroflexi were only detected in freshwater sediment. [Conclusion] These results indicated that bacterial abundance and community structure differed dramatically between freshwater lake and saline lake sediments, and the microbial community composition also differed along the depth of sediments. Our results could provide the scientific base on how microbes in lake ecosystems respond to climate change on the Tibetan Plateau.