Four novel poly(phenylene oxide)-based anion exchange membranes were investigated for electrochemical performance, ionic conductivity and water transport properties in an operating anion exchange membrane fuel cell (AEMFC), using Pt/C gas diffusion electrodes with Tokuyama ionomer. The poly(phenylene oxide)-membranes have a 1- or 5-carbon alkyl spacer between the backbone and a trimethylalkylammonium (TMA) or piperidinium (Pip) cationic group, and ion-exchange capacities (IECs) between 1.5 and 1.9 mequiv g(-1). The polymer with a 5-carbon alkyl spacer, a TMA cationic group, and a higher IEC showed the highest ion conductivity and performance in the AEMFC. The results also show that introducing a 5-carbon alkyl spacer does not improve performance unless the IEC is increased and that exchanging the TMA with a Pip cationic group results in lower fuel cell performance despite a higher IEC. A discrepancy in ion conductivity between fuel cell and ex situ test was observed for the 5-carbon spacer polymers and is attributed to a higher sensitivity for dehydration. Similar water flux under load, from the anode to the cathode with increased water content at both electrodes, was observed for all membranes and only varied with membrane thickness. The deviation in fuel cell performance observed between the membranes could not be explained by differences in water flux or ionic conduction, suggesting that the electrode-membrane interaction plays a major role. Nevertheless, the study emphasizes that high membrane conductivity (for the lambda-range in a fuel cell) and efficient water transport (obtained by lower membrane thickness) promote higher electrochemical performance.