In different regions of Taihu Lake, phosphorus, nitrogen and the microbial biomass C of the sediment were determined, and using the terminal restriction fragment length polymorphism (T-RFLP) technique, bacterial community structures were analyzed. The content of total nitrogen and total phosphorus of sediment No.6 and No.16 were the highest. Trend of various forms of nitrogen and phosphorus with total nitrogen and total phosphorus was basically the same. The result of microbial biomass C showed that No.6 and No.16 were significantly higher than other sites which were similar with each other. Results of T-RFLP showed that there were differences between the bacterial diversity of different regions. Bacterial diversity of No.16 was lowest, but No.1, No.6 and No.7 were higher. Both the composition and the proportion of bacteria from different regions were significantly distinct. In addition, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria which have relationship with cycle of nitrogen and phosphorus are very rich in sediment of all the sites. And Deltaproteobacteria which is related to cycle of sulfur and iron is also rich.