We report results of multiscale simulations of a hydrated ionomer membrane based on sulfonated poly(ether ether ketone) (sPEEK) that constitutes an important class of the promising membrane materials for fuel cell applications. Using atomistic and field-theoretic simulation techniques - classical molecular dynamics and dynamic density functional theory - we study the processes of self-organization in sPEEK membranes in the presence of water. At the same water content, both simulation techniques predict a similar structure of the hydrated membranes. The observed membrane morphology can be represented as a topologically complex sponge-like network consisting of irregular water-filled channels. Compared to Nafion, the channels in the sPEEK membrane are narrower. Nevertheless, the estimated percolation threshold in sPEEK is lower than for Nafion. (C) 2010 Elsevier B.V. All rights reserved.