Resonant Raman and surface-enhanced Raman scattering (SERS) spectroscopies, complemented with scanning tunnel microscopy and electrochemical techniques, have been used to obtain information about the amount and spatial distribution of methylene blue (MB) molecules immobilized on sulfur and four ultrathin molecular alkanethiolate films self-assembled on Au(111) and rough Au electrodes. The intensity of the Raman signals allow one to estimate the amount of immobilized MB at different organic films, whereas the decrease in the SERS intensity as a function of distance for the rough An electrodes is used to locate the average position of the MB species with respect to the Au substrate. We found that significant amounts of cationic MB species are able to diffuse into methyl-terminated thiols, but they are stopped at the outer plane of the self-assembled monolayer (SAM) by negatively charged carboxylate groups. The relative shift of C-N stretching Raman modes indicates that the binding of MB to S is different from that found for MB on thiols. Most of the molecules immobilized on methyl-and carboxylate-terminated thiols are electrochemically inactive, suggesting that strong coupling between the An electrode and the MB molecules is needed for charge transfer. Our results are consistent with a small population of electrochemically active MB species very close to the An surface that reach this position driven by their lipophilic (hydrophobic) character through defects at SAMs.