Abstract: The bacterial compositions in the intestine of freshwater pearl mussel Hyriopsis cumingii and co-cultured fishes (grass carp, Chinese bream, giebel carp, black carp, and bighead carp) in an integrated culture pond were investigated using the method PCR-denaturing gradient gel electrophoresis (PCR-DGGE). The effects of bacteria in water column on intestinal bacteria of the mussel and fishes were analyzed. The results indicated that intestinal bacteria of the mussel and fishes were identified as Firmicutes, Proteobacteria, Actinobacteria, Verrucomicrobia, Cyanobacteria and Fusobacteria. The dominant intestinal bacteria varied among the fishes and mussel. The dominant bacteria were Acinetobacter, Shigella and Mycobacterium in the mussel, and Clostridium in grass carp, and Clostridium and Pseudomonas in Chinese bream, and Acinetobacter and Shigella in giebel carp, and Clostridium and Acinetobacter in black carp, and Acinetobacter and Vibrio in bighead carp. The similarity of intestinal bacterial diversity was high between grass carp and Chinese bream, and between the mussel and giebel carp, which indicated that there were connections between the intestinal bacteria composition and feeding habits of fish. The dominant bacteria in water column was Paenibacillus. The similarity of bacterial diversity was low between water column and intestinal tract of the mussel and fishes, which showed that the effect of bacterioplankton on intestinal bacteria of mussel and fishes was limited.