In order to investigate the community compositions and distribution patterns of bacterioplankton in Lake Dongting and Lake Poyang, and identify their affecting factors, we studied the compositions of aquatic bacteria community of Lake Dongting and Lake Poyang in 57 sampling sites through high-throughput sequencing technology in September 2017. The physical and chemical parameters of these samples were detected. The results showed a total of 20 phyla, 42 classes, 93 orders, 191 families, and 533 genera. At the phylum level, Actinobacteria, Cyanobacteria and Proteobacteria were the main bacteria in Lake Dongting and Lake Poyang. The results of principal component analysis showed that environmental heterogeneity in Lake Poyang was higher than that in Lake Dongting. Mental tests showed that the main factors affecting the compositions of cyanobacteria and other groups were ammonia-nitrogen, nitrate nitrogen, total nitrogen (TN), phosphate phosphorus (PO^3-₄-P), total phosphorus (TP), water temperature (WT), electric conductivity (EC) and salinity (Sal) in Lake Dongting and PO^3-₄-P, WT, EC and Sal in Lake Poyang. The results of the null model showed that the stochastic process was the main driver of aquatic bacteria community assembly. Overall, Lake Poyang was more affected by stochastic process and less deterministic process under higher environmental heterogeneity, whereas Lake Dongting was affected by both stochastic process and deterministic process. Known the spatial distributions and community assembly mechanisms of aquatic bacteria are of great guiding value to the monitoring and evaluation of Lake Dongting and Lake Poyang.