Molecular dynamics (MD) simulation technique was employed to investigate the effect of degree of sulfonation (DS) on structural and dynamical characteristics of sulfonated poly (ether ether ketone) (SPEEK) membranes at different temperatures. MD Simulations were performed for the cell containing SPEEK chains, hydronium ions and water molecules under NVT and NPT conditions. By evaluating the pair correlation functions, it was observed that with increasing the DS of SPEEK, the distance between sulfur atoms increases, more water molecules solvate the sulfur atoms and hydronium ions, the average sulfur hydronium ion separation distance increases and larger water clusters are formed. It was also found that with increasing DS and temperature, the diffusion coefficient and conductivity of hydronium ions enhance. It was also understood, the simulated ionic conductivities qualitatively follow the experimental data. Copyright (C) 2012, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.