Bacterial communities in the water column and sediment of 12 commercial grass carp (Ctenopharyngodon idellus) farming ponds were analysed. At the same time, physical and chemical environmental parameters were measured, including secchi depth (SD), total nitrogen (TN), total phosphorus (TP) and chemical oxygen demand (CODMn). From 12 water samples and 12 sediment samples, 39 different ribotypes were detected with PCR-denaturing gradient gel electrophoresis (PCR-DGGE). The ribotype richness showed that bacterial species in the water column differed among these ponds, and the result of sequencing further revealed the dominant and common bacterial species. In total, 32 bacterial species belonging to seven phyla (Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, Acidobacteria, Fibrobacteres and Fusobacteria) were identified. Ordination via canonical correspondence analysis (CCA) on the DGGE data and environmental parameters indicated that the composition of bacterial community was significantly influenced by SD.