The utilization of different kinds of ion exchange membrane is a common practice in bioelectrochemical systems such as two-chambered microbial fuel cells (MFCs). However, little is known on the effect of the membrane materials on the anodic microbial community diversity.ResultsThe effect of two cationic and one anionic exchange membranes (Nafion N-117, Ultrex CMI-7000, and Ultrex AMI-7000) on the microbial community dynamics of Eubacteria and Archaea has been assessed in two-chambered MFCs. The experimental results indicated that the eubacterial community in the anodic chamber was not affected by the membrane materials, being predominant populations of Bacteroidetes (Porphyromonadaceae) and β-proteobacteria (Alcaligenaceae and Comamonadaceae). On the other hand, the archaeal counterpart appears to be highly dependent on the type of membrane used, as it was evidenced by the selective enrichment of Methanosarcina sp. in the MFC equipped with the membrane Nafion N-117 which was the MFC that showed the highest current production.Conclusions The results obtained in the present study suggest that membrane materials affect archaeal diversity whereas both anodofilic eubacteria and methanogenic archaea populations could play an important role on the overall MFC process performance.