This study demonstrates real-time maximization of power production in a stack of two continuous flow microbial fuel cells (MFCs). To maximize power output, external resistances of two air-cathode membraneless MFCs were controlled by a multiunit optimization algorithm. Multiunit optimization is a recently proposed method that uses multiple similar units to optimize process performance. The experiment demonstrated first convergence toward optimal external resistance and algorithm stability during external perturbations (e.g., temperature variations). Rate of the algorithm convergence was much faster than in traditional maximum power point tracking algorithms (MPPT), which are based on temporal perturbations. A power output of 81-84 mW/L-A (A = anode volume) was achieved in each MFC. (C) 2009 American Institute of Chemical Engineers Biotechnol. Prog., 25: 676-682, 2009