Proton exchange membranes (Nafion) have been studied using current sensing atomic force microscopy to examine the correlation between the surface morphology and the ionic domains, and to probe the local ionic conduction distribution in the membranes. It is found that the local ionic conduction generated from the current sensing images follows a Gaussian-like distribution, with the peak value and the width of the distribution increasing with the relative humidity in the sample chamber and, thus, the water content in the membranes. Two types of Nafion membranes, Nafion 112 and Nafion 117, were studied using the method. The implications of the distribution in relation to the ionic conducting channels in the membranes are discussed.