A membrane electrode assembly (MEA) microbial fuel cell (MFC) with a non-woven paper fabic filter (NWF) was investigated as an alternative to a proton exchange membrane (PEM) separator. The MFC with a NWF generated a cell voltage of 545mV and a maximum power density of 1027mW/m3, which was comparable to that obtained from MFCs with a PEM (551mV, 609mW/m3). The MFC with a NWF showed stable cell performance (550mV) over 300days, whereas, the MFC with PEM performance decreased significantly from 551mV to 415mV due to biofilm formation and chemical precipitation on the membrane surface. Poly [2,5-benzimidazole] (ABPBI) was evaluated with respect to its capacity to increased proton conductivity and contact between separator and electrodes. The overall performance of the MFC with ABPBI was improved by enhancing the ion conductivity and steric contact, producing 766mW/m3 at optimum loading of 50mg ABPBI/cm2.