The increasing global focus on alternative energy sources has led to a renewed interest in fuel cells, especially hydrogen and methanol powered fuel cells. Recent research has shown layer-by-layer (LBL) assembly to be a robust technique for the fabrication of proton exchange membranes with tunable compositions, desired perm-selective properties and high ionic conductivity values. This work describes the optimization of multilayer systems to develop PEMs for use in low-cost direct methanol fuel cells (DMFCs). Here we report that by adjusting the assembly conditions, the relative amounts of each polymer deposited in the film is controlled, which impacts morphological and compositional properties. For example, multilayer films of linear poly(ethylene imine) (LPEI) and sulfonated poly(2,6-dimethyl 1,4-phenylene oxide) (sPPO) assembled from aqueous solution yield ionic conductivity values around 10^-3 S/cm at 100% RH. Since increasing the charge of a polymer decreases its composition in the LBL film, we can maximize the amount of sPPO in the film at low pH values where LPEI is highly charged. The use of aromatic polymers in these membranes reduce methanol crossover, which is a fundamental problem in current methanol fuel cells. Preliminary results indicate these multilayer systems have reduced methanol permeability as compared to NafionŽ membranes.