This study examines methanogen activity in microbial fuel cells when exposed to various environmental stresses, such as oxygen, low pH, low temperature, inhibitor (2-bromoethanesulfonate (BES)), and variations in external resistance. Controlling methanogenesis resulted in an increase in Coulombic efficiency (CE) because it was a major cause of electron loss. Methane was mainly produced from aceticlastic methanogenesis, rather than by syntrophic acetate oxidation, with Methanosarcinaceae being the primary contributor. Lowering the resistance from 600 to 5052 reduced the methanogenic electron loss by 24%; however, changing the temperature or pH level had little effect. A BES injection was the most potent strategy for the selective inhibition of methanogens without damaging exoelectrogens. The addition of 0.1-0.27 mM BES increased the CE from 35% to 70%. Oxygen stress successfully inhibited methanogens, while slightly suppressing the exoelectrogens, and is believed to be a practical option due to its low operating cost. (C) 2010 Elsevier Ltd. All rights reserved.