An atomistic simulation technique is performed to investigate the molecular structure and transport dynamics inside a hydrated Nafion membrane and a hydrated sulfonated poly(ether ether ketone ketone) (SPEEKK) membrane. The simulation system consists of the representative fragments of the polymer electrolytes, hydronium ions and solvent molecules, such as water plus methanol molecules. Simulation results show that the hydrated SPEEKK has less phase separation among hydrophobic and hydrophilic regions in comparison with the Nafion. Those water channels formed in the SPEEKK are much narrower compared to those in the Nafion. These characteristics lead to a lower mobility of hydronium ions and water molecules and hence relatively lower diffusion coefficient of methanol in the SPEEKK. It results in the reduction of the methanol permeation problem in direct methanol fuel cells. (C) 2009 Elsevier B.V. All rights reserved.