Aims: To assess the biodiversity of a large number of microbial fuel cell (MFC) anodes from a variety of MFC designs, all enriched with domestic wastewater, using a molecular fingerprinting method. Methods and Results: We optimized a protocol allowing the rapid characterization of MFC communities using terminal restriction fragment length polymorphism (T-RFLP) with two different sets of primers and a varying number of restriction enzymes. This protocol was further validated by direct comparison with bacterial clone libraries. Twenty-one MFC anodes were analysed by T-RFLP. We also provided a statistical comparison with other bacterial communities from environments sharing common features. Conclusions: Bacterial communities were dominated by beta-Proteobacteria, mostly belonging to the Burkholderiales order, that are known to play an active role in the cycle of metals such as iron and manganese. This property may allow them to properly pass electrons to the anode of an MFC. Significance and Impact of the Study: Unlike other groups, beta-Proteobacteria have seldom been acknowledged as potentially efficient electrochemically active bacteria (EAB) in MFCs. Yet, they are plentiful in natural environments like biocorrosion biofilms and acid mine drainages that consequently show some potential for MFC enrichment.