Surface-enhanced Raman scattering (SERS) of the 4-mercaptopyridine (4-MPy) molecules adsorbed on the electrochemically roughened silver electrodes were investigated under practical electrochemical conditions. The adsorbed 4-MPy molecules are converted from a perpendicular orientation to a parallel orientation as the electrode potential is successively changed from 0 to -1.0 V. The coordination of the nitrogen atom of the pyridine ring to the silver metal weakens the ability of the 4-MPy molecules with a parallel orientation to capture the proton, because of the distribution of the electron density of the nitrogen to the silver metal. The applied potential has a large effect on the protonation/deprotonation process of the adsorbed 4-MPy molecules. More adsorbed 4-MPy molecules are protonated as the electrode potential becomes more negative. This is ascribed to the increase in the charge density on both the electrode surface and the nitrogen atom of the pyridine ring at the negative potentials.