Sulfonated poly(vinylidene fluoride-co-hexafluoro propylene) (SPVdF-co-HFP) and polyaniline (PAni) have shown promise as polymer electrolyte membrane (PEM) materials, especially in direct methanol fuel cells, by virtue of their significantly high ion-exchange capacity (IEC) and membrane selectivity ratio. It was intuited that utilization of PAni nanostructures, with high surface areas, in PEMs can result in further improvement of these attributes. With this objective, positively-charged PAni nanofibers (NFs) were synthesized. Interestingly, when these NFs were exposed to a negatively-charged amphiphile solution for different time extents and followed by washing with an organic solvent, PAni nanowhiskers (NWs) having lengths between 40-120 nm and diameters between 10-40 nm were formed. BET surface area exhibited an increase upon decrease in the aspect ratio of the NFs. Membranes were fabricated using SPVdF-co-HFP as the continuous phase and PAni granules, NFs or NWs as the dispersed phase. SPVdF-co-HFP/PAni NWs and SPVdF-co-HFP/PAni NFs membranes exhibited enhanced IECs, proton conductivities and selectivities compared to SPVdF-co-HFP/PAni granules membrane. However, comparisons between SPVdF-co-HFP/PAni NFs and SPVdF-co-HFP/PAni NWs membranes revealed that the extended conjugation available for the former versus the higher surface area of the latter played a crucial role in determining the uptake and transport properties of the membranes. © The Royal Society of Chemistry.