This work reports a classification analysis method based on the vibrational Raman spectra of 38 quinones and related structures, spectrally ordering and classifying the compounds. The molecular systems are relevant for chemical and biological processes, with applications in pharmacology, toxicology and medicine. The classification strategy uses a combination of principal component analysis with K-means clustering methods. Both theoretical simulations and experimental data are analysed, thus establishing their spectral characteristics, as related to their chemical structures and properties. The protocol introduced here should be broadly applicable in other molecular and solid state systems.