Abstract:[Background] Bacteria are the main drivers in lake ecosystems, and their community structure is highly responsive to the environmental changes in the lake. The special geographical location and high altitude environment of Bangong Lake have shaped a unique microbial ecosystem. However, little is known about the bacteria in this lake. [Objective] To explore the bacterial diversity and distribution pattern in Bangong Lake in the Ali region, we collected samples at 20 sites in the east bank, west bank, center, and bottom of this lake in September 2023. [Methods] The 16S rDNA high-throughput sequencing was performed for the samples, and the α diversity of the microorganisms was measured. The Spearman’s correlation analysis was conducted between the physicochemical properties of water and the α diversity of microorganisms. [Results] A total of 14 886 operational taxonomic units (OTUs) were yielded, indicating 470 genera of 47 phyla. The bacterial community in Bangong Lake was mainly composed of Proteobacteria, Actinomycetota, Bacteroidota, and Verrucomicrobiota. The community had high diversity and richness, with a complex structure. The Spearman correlation coefficient indicated that total phosphorus and electrical conductivity were the main environmental factors affecting the bacteria in Bangong Lake. [Conclusion] This paper clarifies the diversity and distribution pattern of bacteria in Bangong Lake and reveals the water physicochemical factors influencing the bacterial community. The findings provide a reference for studying the dynamics of bacteria after the narrowing or expansion of Bangong Lake in the future.