A new monomer 1,5-bis(4-fluorobenzoyl)-2,6-dimethoxynaphthalene (DMNF) was prepared and further polymerized to form naphthalene-based poly(arylene ether ketone) copolymers containing methoxy groups (MNPAEKs). The side-chain-type sulfortated naphthalene-based poly(arylene ether ketone) copolymers (SNPAEKs) were obtained by demethylation and sulfobutylation. Flexible and tough membranes with reasonably high mechanical strength were prepared. The SNPAEKs membrane showed anisotropic membrane swelling with larger swelling in thickness than in plane. Transmission electron microscopy (TEM) analysis revealed clear nano-phase separated structure of SNPAEKs membranes, which composed of hydrophilic side chain and hydrophobic main-chain domains. Proton conductivities of copolymers increased gradually with increase in temperature. The highest conductivity of 0.179 S/cm was obtained for SNPAEK-80 (IEC = 1.82 mequiv/g) at 80 degrees C, which is higher than that of Nafion117 (0.146 S/cm). The SNPAEKs membranes exhibit the methanol permeability in the range of 3.42 x 10(-8) - 4.49 x 10(-7) cm(2)/s, which are much lower than that of Nafion117. They could be the promising materials as alternative to Nafion membrane for direct methanol fuel cells applications. (C) 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 5772-5783, 2009