Differences in molecular organization of two sides of a chemically symmetric, planar bilayer supported on a Au(111) substrate have been monitored with charge density measurements and in situ polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS). Isotopic substitution of the hydrogen atoms in the hydrocarbon chains with deuterium atoms in one monolayer was employed to allow the monitoring of C-H vibrations from that monolayer alone. Charge density measurements of bilayers formed from dimyristoylphosphatidylethanolamine (DMPE) showed that the effect of placing the deuterated layer next to the substrate or electrolyte had little impact on the electrical barrier properties. In situ PM-IRRAS studies revealed that the structure of the two monolayers was the same at negative potentials, where the bilayer is separated from the Au substrate, but different at more positive potentials or small charge densities, where the bilayer is expected to be directly adsorbed on the Au surface. Thus, the differences observed for the related molecule dimyristoylphosphatidylcholine (DMPC) persist in planar structures, although to a lesser extent. A small but observable variation in the tilt angle was also apparent in the spectra of both isotopically asymmetric DMPE bilayers during the electrochemical phase transition. The fact that this effect was not previously observed for hydrogenous bilayers means that the dynamic behavior of deuterated DMPE and/or of bilayers composed of different monolayers is different from that of hydrogenous DMPE bilayers. These results have implications for future studies in which isotopic substitution is used to extract selectively information from one layer or component of lipid bilayers in spectroscopic or neutron measurements.