Fuel cells are a rapidly developing field of energy conversion technology due to demonstrated high efficiency and low harmful waste products. Multiple tools exist to study and optimize various fuel cell designs; electrochemical impedance spectroscopy (EIS) is a useful tool to characterize internal resistances to transport in electrochemical systems. An EIS study of two fuel cell designs is presented here: proton-exchange membrane (PEMFC) and microbial (MFC) fuel cells. Charge transfer resistances at the anode and cathode electrodes and resistance to proton transport between the electrodes (termed PEM or solution resistance in the PEMFC and MFC, respectively) are of special interest. In addition, the capacitances existing between the electrodes and electrolyte are also studied. Experiments with the PEMFC involved changing the operating conditions and observing the effects on internal resistances and capacitance. MFC experiments involved optimizing the anode bacterial consortium and using different cathode configurations. In all experiments, the resistances in the MFC were much greater than in the PEMFC, usually by 1-2 orders of magnitude.