Abstract: Covalent Organic Frameworks (COFs) or Metal Organic Frameworks (MOFs) are synthesized to transport proton ions in PEM fuel cell applications. The pore size of organic frameworks and the number of sulfonyl functional groups inside their pores are controlled to maximize the proton conductivity and minimize the H2 and O2 crossover thru the membrane. The surface of MOF or COF crystal flakes is chemically modified to improve the mixability with polymer binder and this avoids the formation of physical defects or voids between polymer binder and crystals. The proton conducing membrane is made by dissolving a polymer binder in a solvent and then adding the chemically modified flakes into the solution and forming it into a film. The MOF or COF flakes can also be coated onto the proton conducting polymer membranes or continuously grown into larger size of films in solutions.