Proton exchange membranes (PEMs) are usually used in two-chambered microbial fuel cells (MFCs) to keep the anode and cathode liquids/gases separate. The membranes allow protons migrate to the cathode from the anode but prevent dissolved oxygen transferring from the cathode to the anode. The disadvantages of membranes in MFCs are expensive and some degree of decreasing performance. Thus, the objective of the study is to investigate the operating performance of different membranes used in MFC. An exoelectrogen Pseudomonas aeruginosa YC5 was inoculated to a two-chambered MFC with graphite felt electrodes to evaluate system performance in this study. Acetate solution (10,000 mg/L) and 80 mM phosphate solution were prepared by a combined anolyte and catholyte. The maximum power densities produced by PEM (Nafion), anion exchange membrane (AEM), ultrafiltration membrane (UFM) with molecular weight cut offs of 1K daltons, and cling film were 186, 170, 125, and 37 mW/m2, respectively. The internal resistances (Rint) attributable to these membranes (Nafion, AEM, UFM, cling film) were 340, 412, 476, 17,200 Ω, respectively. Accordingly, a low internal resistance in MFC would result in high power density. It is noted that although the maximum power density produced by cling film is 5 times smaller than it produced by Nafion, cost of cling film was only 10,000 lower than that of professional membranes. Thus, the cling film has a potential for being applied in large scale MFC plant for wastewater treatment. In the future, the performance of the large scale MFC with cling film to treat wastewater and produce electricity will be evaluated.