Four microbial fuel cells (MFCs) inoculated with different bacterial species were constructed. The species were Pseudomonas putida, Comamonas testosteroni, Corynebacterium gultamicum, and Arthrobacter polychromogenes. The MFCs were operated under identical continuous flow conditions. The factors affecting the capabilities of the MFCs for treating organic matter and generating power were evaluated and compared. The factors include microbial species type, organic loading, and substrate degradation rate. For all four MFCs, power output increased with the organic loading rate. Power density also increased with the substrate degradation rate. These findings implied that more organic matter was utilized for power generation at higher organic loading and substrate degradation rates. However, coulombic efficiency increased with decreased organic loading and substrate degradation rates. Apparently, all four MFCs had low efficiencies in generating power from organic matter. These low efficiencies are attributed to the long distance between the anode and the cathode, as well as to the small ratio of the proton exchange membrane surface area to the anode chamber surface area. These features may have caused most of the protons produced in the anode chamber to leave the chamber with the effluent, which led to the low power generation performance of the MFCs.