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Novel polyelectrolyte membranes were prepared from pure solutions of alginate (Alg), carrageenan (Car) and their mixtures. The films were crosslinked and sulfonated and then, characterized by several techniques: ionic exchange capacity (IEC), water uptake, mechanical thermal properties, and also functional properties such as methanol permeability and proton conductivity. The results show that Alg/Car membranes have a ductile behavior. Low carrageenan concentrations have a weak thermoprotective effect, which slightly delays both Tg and Tm of prepared membranes. The methanol permeability of Alg/Car membranes increase with the carrageenan content varying from 0.55 × 10−6 cm2 s−1 for Alg/Car 100/00 to 4.89 × 10−6 cm2 s−1 for Alg/Car 80/20. The Proton conductivities of the membranes increase with the carrageenan content from 9.79 × 10−3 S cm−1 for Alg/Car 100/00 until 3.16 × 10−2 S cm−1 for Alg/Car 80/20 at 90 °C. Finally the proton transfer mechanism is discussed in terms of the conductivity activation energy and the dependence of the proton diffusion coefficient with the temperature has been studied.