The morphology of proton conducting membranes based on sulfonated poly(aryl ether ketone) (SPAEK-6F) and recast Nafion membranes containing hydrophilic/hydrophobic ionic liquids has been investigated by small-angle X-ray scattering (SAXS) and tapping mode atomic force microscopy (TM-AFM). The hydrophilic/hydrophobic nature of the ionic liquid has been found to affect the morphology, conductivity and thermal stability of the membranes. The small angle upturn in scattering intensity at very low angles observed in SAXS for different membranes suggests the presence of large scale fluctuations, whereas the absence of ionomer peak for membranes based on SPAEK-6F is possibly due to the higher rigidity of hydrophobic part of the polymer despite the presence of ionic domains. The correlation between morphology and properties of different membranes containing ionic liquids will be helpful in improving the design of proton conducting membranes containing ionic liquids for applications in polymer electrolyte fuel cells (PEFCs) at medium (100-200 degrees C) temperatures and under anhydrous conditions.