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Seeds of domesticated Vicia (vetch) species (family Fabaceae-Faboideae) are produced and consumed worldwide for their nutritional value. Seed accessions belonging to 16 different species of Vicia—both domesticated and wild taxa—were subjected to a chemotaxonomic study using ultraperformance liquid chromatography–mass spectrometry (UPLC-MS) analyzed by chemometrics. A total of 89 metabolites were observed in the examined Vicia accessions. Seventy-eight out of the 89 detected metabolites were annotated. Metabolites quantified belonged to several classes, viz., flavonoids, procyanidins, prodelphinidins, anthocyanins, stilbenes, dihydrochalcones, phenolic acids, coumarins, alkaloids, jasmonates, fatty acids, terpenoids, and cyanogenics, with flavonoids and fatty acids amounting to the major classes. Flavonoids, fatty acids, and anthocyanins showed up as potential chemotaxonomic markers in Vicia species discrimination. Fatty acids were more enriched in Vicia faba specimens, while the abundance of flavonoids was the highest in Vicia parviflora. Anthocyanins allowed for discrimination between Vicia hirsuta and Vicia sepium. To the best of our knowledge, this is the first report on employing UPLC-MS metabolomics to discern the diversity of metabolites at the intrageneric level among Vicia species.