There are numerous microorganisms, especial pathogens, in the discharges. Those microorganisms are discharged into the river and sea through sewage outfalls, which results in possible health risks to coastal populations. And more attention should be paid to municipal discharges in developing countries. This study investigated the microbial community in the discharges by constructing 16S rDNA clones library and using the PCR-RFLP technology. Phylogenetic analysis of bacteria in municipal discharges showed that there were 59 species, which were divided into 11 classes. Proteobacteria accounted for 85% of all the bacteria, of which β-Proteobacteria and γ- Proteobacteria were the dominant classes. Bacteria in the waste water treating process had important influence on microbial community in municipal discharges, therefore, municipal sewage plant should choose the process according to the characteristics and purifying capacity of the receiving water body. Legionella spp. accounted for approximately 10% , the Legionnaires' disease resulted from which might be of top risk for the residents in the surrounding of the municipal discharges outfall and receiving water. Dechloromonas aromatica could make use of chlorite ( CIO - ) , which led to its survival from chlorine disinfection, and it alerted us that several disinfection methods should be used together to ensure the bacterial safety of municipal discharges. Coliform group and other pathogenic bacteria, such as Salmonella spp. , Shigella spp. , Escherichia coli, Vibrio cholerae, Staphylococcus aureus, Arcobacter spp. were not detected in this study, and it indicated that we should do more work and use more methods to investigate the perniciousness of discharges.