The microbial communities of operating membraneless microbial fuel cells has been analyzed sampling different sites, from the anaerobic anode to the aerobic area of the cathode, using the fingerprinting molecular technique, DGGE (Denaturing gradient gel electrophoresis). The anode materials sampled were: carbon fibres of a brush, carbon cloth and stainless steel chips (AISI 304). The cathodes were carbon cloth based. The microbial fuel cells were inoculated with row wastewater coming from a municipal plant of Milan city and weekly fed with sodium acetate 3 g/l. DGGE profiles enabled to calculate the Jaccard similarity indexes for the bacterial communities that developed between the electrodes of the MFCs. In this way the degree of selection of microbial communities was defined in relation to the constructive characteristics, materials used and distance between the electrodes The cluster analysis based on similarity data, showed that the microbial populations, coming from the same inoculum, gradually diverged in relation to the structural characteristics of the cell, as well as to the material and the geometry of the anode. In addition, the excision and sequencing of some bands permitted the characterization of the different communities and bacteria groups.