In order to investigate the spatial and vertical change of bacteria community structure in the Pearl River estuary sediment, denaturing gradient gel electrophoresis (DGGE) and multivariate statistical analyses were carried out in this study. Results of multidimensional scaling analyses (MDS) were in good agreement with the DGGE band patterns suggesting that vertical depth had a significant impact on sediment bacterial community structure except sample A2. Canonical correspondence analysis (CCA) was also conducted to infer the relationship between environmental variables and bacterial community structure. Bacterial phylotypes in different stations were closely related uniquely to the overlying water environment. Salinity, pH, ammonium, phosphate and silicate were considered to be the key factors driving the changes in bacterial community composition. The neighbour-joining analysis divided bacteria sequences into eight groups, Proteobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, Firmicutes, Planctomycetales and Cyanobacteria. Sequencing analysis results suggested that Proteobacteria and Bacteroidetes were the dominant bacterial groups in the four sediment samples.Key words: Bacterial community structure, the Pearl River estuary, denaturing gradient gel electrophoresis (DGGE), multivariate statistical analysis.