Microbial community dynamics and its electron transfer process within a biocathode in a microbial fuel cell (MFC) were investigated in this study. The MFC was operated steadily over 400 days, and the power density reached 1.92 and 10.27W/m3 based on the reduction of nitrate and oxygen, respectively. The six major groups of the clones that were categorized among the 26 clone types were Proteobacteria, Bacteroidetes, Actinobacteria, Planctomycetes, Firmicutes and uncultured bacteria. Microbial community dynamics showed that Betaproteobacteria was replaced by Gammaproteobacteria as the most abundant division among all the clone types with a percentage of 48.86% in the cathode compartment, followed by 20.45% of uncultured bacteria, 17.05% of Bacteroidetes, and others. Distinct oxidation and reduction peaks could be observed in the profiles of cathodic effluent during the cyclic and differential pulse voltammetry tests. It confirmed that nitrate and oxygen reduction in the cathode compartment could be significantly enhanced by the presence of microbes, which are able to excrete metabolites to assist the electron transfer process either in the anode or in the cathode compartment.