The composition, abundance and diversity of anodic microbial communities in three parallel-operated MFCs, which inoculated with activated sludge, were investigated by 16S rDNA based high-throughput sequencing. The relationship between the microbial populations and MFC efficiency was evaluated. The efficiency of MFCs was markedly different even if these MFCs were started up and operated under the same conditions. Two of them (named after Mfc-1 and Mfc-3)arrived at the maximum voltage of 220 to 240 mV with power density of 1.85 to 2.33 W/m³. However, the maximum voltage of MFC Mfc-2 was relative low and kept at about 120 mV. Microbial community composition and abundance were significantly different even if they were enriched by the same substrate. Highly abundant bacteria, such as Anaeromusa, Dechloromonas, Geobacter, that are capable of producing electricity were enriched in Mfc-1 and Mfc-3. However, the genus Acinetobacter, a non-electrogen, existed at high abundance in the Mfc-2. This study concluded that divergence of dominant anodic microbial groups in MFCs, due to possible mismanagement and reactor design drawbacks, resulted in the difference of electricity-producing efficiency. To improve the reliability of experimental results during investigating the MFC function and its influencing factors, at least three parallel-operated MFCs were preferred.