Abstract:[Objective] To explore the composition and diversity of sulfur-oxidizing bacteria (SOB) community and its response to environmental variables in the mainstream and branches of the Three Gorges Reservoir (TGR). [Methods] A total of nine sampling locations were selected along the mainstream and branches of the TGR in March 2017. The physical and chemical parameters were measured on the sampled waters, followed by soxB gene-based phylogenetic analyses. The correlation analysis was performed between the physicochemical properties of the sampled waters and the composition and diversity of sulfur-oxidizing bacterial community. [Results] SOB in the collocted TGR waters belonged to α-Proteobacteria and β-Proteobacteria, with the the latter being dominant (relative abundance was higher than 95.6% in the studied mainstream and branch samples). Cluster analysis and principal coordinate analysis (PCoA) showed that the branch samples are scattered with each other and with their corresponding mainstream sample, while the mainstream sampls are relatively more centralized. The Mantel test showed that the SOB population composition was significantly (P < 0.05) correlated with the measured physicochemical parameters (i.e. water temperature, salinity, dissolved oxygen, algal content and pH) of the water samples. Pearson correlation analysis showed that the community diversity of sulfur-oxidizing bacteria was negatively correlated with algal content and dissolved inorganic carbon (DIC). [Conclusion] The SOB in the branch and mainstream TGR waters mainly belongs to the Proteobacteria. The composition of the SOB populations is similar among the mainstream samples, whereas the SOB population composition in the branch samples differs with each other and with their corresponding mainstream samples. This situation is mainly caused by the characteristic physical and chemical properties of the TGR waters.