Liquid chromatography coupled to high-resolution mass spectrometry (LC-Q/TOF) is a powerful tool to perform chemotaxonomic studies through identification of grape secondary metabolites. In the present work, the metabolomes of four autochthonous Italian red grape varieties including the chemical classes of anthocyanins, flavonols/flavanols/flavanones, and terpenol glycosides, were studied. By using this information, the metabolites that can potentially be used as chemical markers for the traceability of the corresponding wines were proposed. In Raboso wines, relatively high abundance of both anthocyanic and non-anthocyanic acyl derivatives, is expected. Potentially, Primitivo wines are characterized by high tri-substituted flavonoids, while Corvina wines are characterized by higher di-substituted compounds and lower acyl derivatives. Negro Amaro wine’s volatile fraction is characterized by free monoterpenes, such as α-terpineol, linalool, geraniol, and Ho-diendiol I. A similar approach can be applied for the traceability of other high-quality wines.