Microbial fuel cells (MFCs) fed with wastewater are currently considered a feasible strategy for production of renewable electricity at low cost. A membrane-less MFC with biological cathode was built from a compact wastewater treatment reactor. When operated with an external resistance of 250 Ohm, the MFC produced a long-term power of approximately 70 mW/m2 for ten months. Denaturing Gradient Gel Electrophoresis (DGGE) analysis of the cathode biomass when the MFC was closed on a 2100 Ohm external resistance showed that the sequenced bands were affiliated with Firmicutes, -Proteobacteria, -Proteobacteria, -Proteobacteria, and Bacteroidetes groups. When the external resistance was varied between 250 and 2100 Ohm, sustainable resistance decreased from 900 to 750 Ohm, while sustainable power output decreased from 32 to 28 mW/m2. It is likely that these effects were caused by changes in the microbial ecology of anodic and cathodic biomass attached to the electrodes. Results suggest that cathodic biomass enrichment in “electroactive” bacteria may improve MFCs power output in a similar fashion to what has been already observed for anodic biomass.