We describe a proton exchange membrane (PEM) system in which the self-organization of molecular precursors generates directional proton layers of high ionic group content in a scaffolding hydrophobic hybrid material. In particular, the use of the self-assembling strategy of molecular precursors is noteworthy and we have shown in this paper that it led to self-organized directional proton layers along hundreds of nanometers. The PEM hybrid membranes are homogeneous, flexible and show both thermal and chemical stability. They were surveyed for their ability to form proton layers reaching high ionic conductivities. The simple synthesis procedure and good conductivity/methanol permeability selectivity suggest that the hybrid membranes may be promising candidates for use in DMFCs