Polyelectrolyte membranes based on Nafion (R) and bio-functionalized montmorillonite (BMMT) with chitosan biopolymer, as polycationic intercalant were fabricated by solvent casting method. X-ray diffraction analysis confirmed the exfoliated structure of clay. Methanol permeability results revealed that the presence of 10wt% BMMT in synthesized nanohybrid membranes can reduce the permeability to 5.72 x 10(-8) cm(2) s(-1) in comparison with 2.00 x 10(-6) for that of Nafion (R) 117. However proton conductivity of nanohybrids was decreasing with increasing BMMT loading, but obtained values were indicating the lower sacrificing of conductivity in comparison with membranes based on unmodified MMT. According to selectivity parameter, membranes containing 2wt% of BMMT showed optimum properties. it was suggested that improvement of transportation properties could be due to the electrostatic interaction between amino groups of chitosan and Nafion (R) sulfone groups. Considering the suitable thermal stability, low methanol crossover and appropriate proton conductivity properties, Nafion (R)/BMMT nanohybrid membranes, could be proposed as novel polyelectrolytes for direct methanol fuel cell application. (C) 2009 Elsevier B.V. All rights reserved.