The imidazole group of a histidine side chain has four different protonation forms, i.e., the two neutral tautomers (N1- and N3-protonated forms), imidazolium cation, and imidazolate anion. Owing to the presence of these convertible protonation forms, histidine plays important: roles in proton-transfer reactions in various enzymes. Vibrational spectroscopy is one of the most powerful methods to study the protonation state of histidine in proteins. For systematic investigation of IR and Raman markers of the protonation state of histidine, we have performed ab initio normal-mode calculations using the density function theory (DFT) method for all of the four protonation forms of 4-methylimidazole (a simple model compound of a histidine side chain) and their N-deuterated analogues. FTIR and Raman spectra of all of these compounds were measured, and the observed bands were assigned according to the calculated frequencies and intensities. Differences in the optimized geometries and changes in the vibrational couplings explained the differences in band frequencies and N-deuteration shifts among the protonation forms. These analyses provided theoretical bases for the IR and Raman markers of the protonation state, including known markers, such as the C4C5 stretching and the C5N1 stretching bands, as well as some new potential markers.