Abstract: To investigate the effect of fish aquaculture on microbial community structure in sediments of aquaculture pond, we selected two common types of aquaculture fish, grass carp (Ctenopharyngodon idellus) and hybrid snakehead (Channa maculate♀×Channa arguss♂), to analyze the microorganisms of the sediment by PCR and denaturing gel gradient electrophoresis (DGGE). Seventy-two DGGE bands were found in the sediments of the two aquaculture fish, among which 67 bands were found in grass carp enclosures and 70 bands in hybrid snakehead enclosures. Thirty-seven bands were sequenced, and a total of 48 sequences were obtained. Proteobacteria dominated the microbial community in species richness (52.8%). Microbial community structure analysis shows significant difference between the two aquaculture patterns. The Shannon-Weiner index and Simpson index were different between these two fish, with Shannon-Weiner index higher in hybrid snakehead aquaculture than in grass carp aquaculture. Thus, different nutrient feeds and lifestyles of species also influence microbial community structure. The monthly changes of the two fish exhibited no significant difference, which shows that the microbial community structure changes little in breeding process.