A new sulfonated copolymers containing congo red groups were synthesized as a potential electrolyte for high temperature PEFCs. The resulting cross-linked sulfonated hybrid congo red membranes showed greatly improved water stability in comparison with the uncrosslinked ones while high proton conductivity was maintained. sulfonated membranes have been tested with respect to fuel cell performance. Short term fuel cell test for 100 hr gave a stable performance. These membranes are less expensive compared to Nafion. New sulfonated proton exchange composites membranes were used biological fuel cells. Molasses which is the waste of sugar factory, was used in anode as fuel and different bacteria species was sowing. Potential change was reported in biological fuel cells.