The major problems of polymer electrolyte membrane fuel cell technology that need to be highlighted are fuel crossovers (e.g., methanol or hydrogen leaking across fuel cell membranes), CO poisoning, low durability, and high cost. Chitosan and alginate-based biopolymer membranes have recently been used to solve these problems with promising results. Current research in biopolymer membrane materials and systems has focused on the following: 1) the development of novel and efficient biopolymer materials; and 2) increasing the processing capacity of membrane operations. Consequently, chitosan and alginate-based biopolymers seek to enhance fuel cell performance by improving proton conductivity, membrane durability, and reducing fuel crossover and electro-osmotic drag. There are four groups of chitosan-based membranes (categorized according to their reaction and preparation): self-cross-linked and salt-complexed chitosans, chitosan-based polymer blends, chitosan/inorganic filler composites, and chitosan/polymer composites. There are only three alginate-based membranes that have been synthesized for fuel cell application. This work aims to review the state-of-the-art in the growth of chitosan and alginate-based biopolymer membranes for fuel cell applications.