Oligosaline lakes in arid regions provide indispensable water resources for humans; however, information on the bacterial community composition (BCC) of this ecosystem is limited. In the present study, we explored seasonal and vertical variations in BCC in Lake Bosten, a unique oligosaline lake (1.2‰ salinity) in arid, northwestern China, using denaturing gradient gel electrophoresis and 16S rRNA gene sequencing. We obtained 544 clones and 98 operational taxonomic units (OTUs) from six clone libraries. The top 10 OTUs represented 59.4% of the entire bacterial community. Betaproteobacteria (22.1%), Gammaproteobacteria (19.9%), Bacteroidetes (18.8%), and Firmicutes (11.4%) dominated in Lake Bosten. Although seasonal variations were recorded in BCC, the vertical changes observed were not significant. Water temperature and salinity were the most important factors shaping the dynamics of BCC. A low degree of overlap was observed in BCC between Lake Bosten and freshwater ecosystems, especially for Betaproteobacteria and Bacteroidetes. An RDP seqmatch analysis showed that 169 sequences (31%) were novel bacterial sequences (<97% similarity to the closest sequences in GenBank), which suggested that specific indigenous bacteria inhabit this oligosaline environment. Our results support bacterial endemicity being more common than previously considered, particularly in oligosaline lakes. An analysis of these communities may reveal how bacteria respond to increases in salinity and nutrients in the early stage of salinization and eutrophication.