A new type of fuel cell that combines the advantages of a proton exchange membrane fuel cells and anion exchange membrane fuel cells operated with methanol is demonstrated. Two configurations: one with a high pH anode and low pH cathode (anode hybrid fuel cell (AHFC)),and another with a high pH cathode and a low pH anode (cathode hybrid fuel cell (CHFC)) have been studied in this work. The principle of operation of the hybrid fuel cells were explained. The two different hybrid cell configurations were used in order to study the effect of the electrode fabrication on fuel cell performance. Further, the ionomer content and properties such as the ion exchange capacity and molecular weight were optimized for the best performance. A comparison of the different ionomers with similar properties is carried out in order to obtain the best possible ionomer for the fuel cell. An initial voltage drop was observed at low current density in the AHFC, this was attributed to the alkaline anode and the effect of the ionomers with the new cationic groups were studied on this voltage drop was studied. These ionomers with the different cationic groups were studied in the CHFC design as well. Finally, the use of non platinum catalyst cathode with the CHFC design was also demonstrated for the first time.