Potential and illumination regulate the acclimation and growth of exoelectrogenic photosynthetic bacteria in bioelectrochemical systems. To understand the influence of potential on the bacteria community diversity under illumination, PCR-based molecular ecological techniques including denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) were applied to evaluate the bacteria community diversity of biofilm on working electrode. Four potentials of 0, 0.2, 0.4 and 0.6 V (vs. Ag/AgCl) were applied to the working electrode. The DGGE results showed that the band number of the biofilm at 0.6 V was dramatically lower than those at other potentials. The sequencing analysis of these hands showed that most of them belonged to classes of alpha-Proteobacteria, beta-Proteobacteria and Clostridia. The T-RFLP results showed that the number of T-RFs was the largest at 0.2 V and then decreased with increasing potentials. Although the application of DGGE or T-RFLP resulted in different bacterial diversities, both techniques revealed that potential dramatically affected the bacterial diversity and high potential decreased the diversity.