Bacterial community structure and the effects of several environmental factors on the microbial community distribution were investigated in the sediment of the eutrophic Lake Xuanwu. Profiles of bacterial communities were generated using denaturing gradient gel electrophoresis (DGGE), and the results were interpreted with multivariate statistical analysis. Five major variables in sediment were examined in a principal component analysis, which indicates notable differences of physicochemical parameters among different sites of the lake. To assess changes in the genetic diversity of bacterial communities of different sampling sites, DGGE band patterns were analyzed by multidimensional scaling analysis, which indicated that sampling sites having similar environmental characteristics also have the similar microbial communities. Canonical correspondence analysis demonstrated that pH and redox potential had significant effects on the bacterial community composition in the sediments. Analysis of DNA sequences revealed that the dominant bacterial groups in Lake Xuanwu belonged to Proteobacteria, Actinobacteria, Verrucomicrobia, and Nitrospirae, which are commonly isolated from freshwater ecosystems.