Perfluorosulphonic acid-based membranes such as Nafion are widely used in fuel cell applications. However, these membranes have several drawbacks, including high expense, non-eco-friendliness, and low proton conductivity under anhydrous conditions. Biopolymer-based membranes, such as chitosan (CS), cellulose, and carrageenan, are popular. They have been introduced and are being studied as alternative materials for enhancing fuel cell performance, because they are environmentally friendly and economical. Modifications that will enhance the proton conductivity of biopolymer-based membranes have been performed. Ionic liquids, which are good electrolytes, are studied for their potential to improve the ionic conductivity and thermal stability of fuel cell applications. This review summarizes the development and evolution of CS biopolymer-based membranes and ionic liquids in fuel cell applications over the past decade. It also focuses on the improved performances of fuel cell applications using biopolymer-based membranes and ionic liquids as promising clean energy. Int. J. Mol. Sci. 2020, 21, 632 2 of 52 used to exchange protons from the anode to the cathode [1]. PEMFCs are light, highly efficient, and compact. They operate at relatively low temperatures (≈80 • C), have high power density, and are suitable for various applications. Figure 1 shows that PEMFC consists of various important elements, namely, bipolar plates, diffusion layers, electrodes (anode and cathode), and an electrolyte. The core of a PEMFC is a membrane electrode assembly (MEA) composed of a proton exchange membrane (PEM) placed between two electrodes. Int. J. Mol. Sci. 2019, 20, x FOR PEER REVIEW 2 of 53 Int. J. Mol. Sci. 2020, 21, 632 3 of 52Polysaccharides, such as chitosan (CS) and cellulose, are among the best natural polymer materials because of their abundance in the environment. CS is a linear polysaccharide consisting of randomly distributed β-(1-4)-linked d-glucosamine (deacetylated unit) and N-acetyl-d-glucosamine (acetylated unit), which is produced by the deacetylation of chitin. CS has high water affinity properties as there is the presence of three different polar functional groups, which are hydroxyl (-OH), primary amine (-NH 2 ), and C-O-C groups. CS has a structure that is very similar to cellulose, but the difference among them is that CS contains amine groups and its structure is characterized by its molecular weight and degree of deacetylation, where its solubility is depended on [7].CS has rigid structure and high crystallinity as there are three hydrogen atoms strongly bonded between the amino and hydroxyl groups within the CS monomers, due to the immobilized structure, which leads to its proton conduction limitation. Moreover, CS has attractive physicochemical properties in aqueous solution due to its polycationic nature and this leads to wide range of biological purposes such as antimicrobial activity and disease resistance activities in plants [8]. CS membranes are one of the most preferable and favorable materials to re...