A material-sensitive atomic force microscopic (AFM) tapping mode was combined with current measurements to investigate structure, phase separation, and conductive structure of surfaces and cross sections of long side chain Nafion and short side chain AQUIVION PFSA ionomer membranes. We found unexpected large-scale ordered structures consistent with a dominant lamellar polymer structure at the cross sections. The highly terraced areas of both ionomers have a wide distribution of layer thicknesses from sub-nanometer to a few nanometers. In both broad size distributions, preferential sizes were identified that reflect the different lengths of the molecular side chains, indicating a stacking in layers. The nanoscale phase separation of the ionomer was analyzed by using the capacitive current distribution. In AQUIVION PFSA, larger connected water-rich ionic areas were found than in Nafion with same total ionic area. A steady-state current at the cross sections evolved only after an activation period by enforcing current flow though the membrane. A comprehensive and heterogeneous current distribution was observed with highly conductive areas. In contrast, on outer membrane surfaces, only non-continuous spot-like currents were observed. In general, our measurements are consistent with conduction in water layers in-between polymer chains and a bi-continuous structure under faradaic current flow. (C) The Author(s) 2014. Published by ECS. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives 4.0 License (CC BY-NC-ND, http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is not changed in any way and is properly cited. For permission for commercial reuse, please email: [email protected]. All rights reserved.