The bacterial diversity in three aquacultural systems in Shaotan river reservoir of Wuhan city was studied by the method of 16S rDNA clone library.The grass crap,silver carp,and gible carp were basal groups of the 3 aquacultural systems,while the paddlefish and big head carp were added by different proportions.No paddlefish and 6% big head carp was named system 1,while 3% paddlefish and 3% big head carp was named system 2,and 6% paddlefish and no big head carp was named system 3.The result of phylogenetic analysis showed that the sequences of 16S rDNA clone library in three aquacultural systems included 10 bacterial communities:Proteobacteria,Bacteroidetes,Cyanobacteria,Planctomycetes,Verrucomicrobia,Actinobacteria,Acidobacteria,Chloroflexi,Fusobacteria and OP10.The multifarious analysis demonstrated that the diversity index of system 2 was better than the other aquacultural systems,while the diversty index of system 3 was better than system 1.