Abstract: The bacterial community composition in the substrate-biofilm shrimp culture system was monitored and investigated by pcr-denaturing gradient gel electrophoresis (DGGE). Results show that: 1) The water flora structure of substrate group was less diversified than that of the control. 2) The similarity coefficient of substrate group increased with time, while that of the control increased first then decreased. 3) Uncultured Firmicutes (Bacillus spp.), the dominant bacteria at the beginning of culture in the control, were uncultured Proteobacteria and uncultured bacterium, and the dominant bacteria at the end of culture was uncultured Firmicutes (Bacillus spp.). Uncultured Firmicutes (Bacillus spp.) and uncultured bacterium were the dominant bacteria throughout the culturing period. The results provide references for clarifying the function and mechanism of ecological control of microbes in artificial substrate system.