The effect of weight ratio of Chitosan (CH) to Pectin (PEC) is studied. The methanol permeability of CH/PEC membranes decreases with the amount of Pectin. Proton conductivities of CH/PEC membranes decrease until a ratio composition of 1:1. DSC studies reveal excision of ionic pairs between carboxylic and ammonium groups. Proton diffusion coefficients decrease one order of magnitude in CH/PEC membranes.