Abstract: To explore the effect of cyanobacterial blooms to the planktonic bacteria community composition, a sample survey was conducted in Xiaojiang River, a tributary of the Three Gorges Reservoir. We found that Anabaena flosaquae and Microcystis aeruginosa were the dominant species of cyanobacterial blooms with 67% and 26% of tota species in the Xiaojiang River, respectively. The density of cells is 6.22109/L and 8.77108/L, respectively. During the process of cyanobacterial blooms, the community of planktonic bacteria changed significantly. The dominant bacteria in mid and end of blooms were Roseomonas and Bacillus respectively. In addition, the relative abundance of Proteobacteria and Actinobacteria increased significantly in the end of blooms. These results suggest the correlation between the planktonic bacterial community composition and cyanobacterial blooms.