A number of 2-methylthio-6-methyl-4-alkyl- and alkylaminopyrimidines, as well as their salts produced by the reaction with methyl p-toluenesulfonate and trifluoroacetic acid, were investigated. The quantum chemical and experimental IR and Raman spectral methods were used to determine the preferential isomeric forms of the molecules of studied compounds, whose convenient spectral markers were revealed. The starting pyrimidines and their salts were found to exist predominantly as an amino form. The salt formation proceeds via the methylation (protonation) of the N atom of pyrimidine ring.