To study the effect of cathode type on performance and microbial diversity of the MFC, aerobic biocathode and air-cathode were incorporated into microbial fuel cells (MFCs) which were explored for simultaneous azo dye decolorization and electricity generation. The electrochemical impedance spectroscopy (EIS) results demonstrated that the catalytic activity of the microorganisms on the biocathode surface was comparable with that of the platinum coated on the air-cathode. The power density achieved by using biocathode was lower than air-cathode, but the biocathode could greatly improve the Congo red decolorization rate. By using the biocathode, 96.4% decolorization of Congo red was obtained within 29 h, whereas, about 107 h was required to achieve the same decolorization efficiency with the air-cathode. 16S rRNA sequencing analysis demonstrated a phylogenetic diversity in the communities of the anode biofilm and showed clear differences between the anode-attached populations in the MFCs with a different cathode type.