An ion exchange membrane is a polymer matrix of cross-linked polyvinyl chloride macromolecular chains, on which are grafted ionic functional sites. The transport numbers of two metal ions and proton through these membranes were determined using the well-known electrochemical Hittorf's method. The cation exchange membrane Nafion, having sulfonic reactional site (-SO3-), yielded the transport number of copper relatively less than that of sodium, leaving way to proton to be transported. In contrast, the anion membrane of alkyl ammonium reactional site (-NR4+) prevented the transfer of cation metals and allowed the proton to displace by defect of permselectivity. These two membranes were used as separators in microbial fuel cells (MFC). In effect, the MFC with the anion membrane AMX, gave relatively higher power density (1.10mW/m(2)) compared to the cation exchange membrane Nafion (0.45mW/m(2)). Really, with the AMX separator, the metal ions present in the wastewater anolyte compartment were blocked by the membrane giving way to the protons to displace freely and be reduced efficiently at the cathode. In the mono-compartment cell, the ions moved sideways between anode and cathode, yielding the highest power density (11.90mW/m(2)) so far obtained. The pH adjustment of anolyte and cathode compartments support, therefore, strongly the cell voltage evolutions. In addition, the cyclic voltammetry results showed that the electroactive biofilm of the bioanode using the AMX membrane described a diffusion-limited process, while that of the Nafion membrane made in evidence the adsorption monolayer of redox species. Besides, the electrochemical impedance spectroscopy revealed that the charge transfer resistance at the interface bioanode/biofilm decreased drastically from 728 to 18cm(2) for Nafion MFC during 11 days of functioning.