Random amplified polymorphic DNA (RAPD) genomic analyses and chemical composition have been applied to the identification and authentication of Tropea Red onion, a typical italian product with Protected Geographical Indication. Amplification of genomic DNA using 60 random primers highlighted a good clustering differentiating Tropea Red onion from three commercial reference samples used in our study (Saratoga, a yellow onion; Crystal, a white onion; Primula Rossa, a red variety), underlining the existence of intervarietal genetic difference. The antioxidant properties of onions was also investigated. Antioxidant capacity, assessed by three different methods (DPPH, ABTS and photochemiluminescence both with ACL and ACW mode) showed a highest antioxidant activity of Primula Rossa. The antioxidant properties may be correlated to the large amount of polyphenols and flavonoids contained. The analysis of total phenolics content was performed by using the Folin Ciocalteu methods corroborated the same tends of antioxidant capacity. Quercetin and glucosides forms in onion varieties were characterized and quantified using high-performance liquid cromathography (HPLC) at 365 nm. On the basis of our results, flavonoid profiles seems to be variety specific, showing same differences between cultivars