Betanidin is a basic betacyanin with a 5,6-dihydroxyl moiety which causes its high antioxidant activity. For the purpose of structural study, the enzymatic oxidation of betanidin and betanin (5-O-glucosylated betanidin), followed by chromatographic separation of the oxidation products with spectrophotometric and mass spectrometric detection (LC-DAD-MS/MS) was performed. Within the pH 4-8 range, two main oxidation peaks of betanidin were observed, betanidin quinonoid (possibly betanidin o-quinone) and 2-decarboxy-2,3-dehydrobetanidin, whereas at pH 3 only dehydrogenated and decarboxylated derivatives were detected, suggesting different stabilities of the products at different pH values. The presence of two prominent oxidation products, 2-decarboxy-2,3-dehydrobetanidin and 2,17-bidecarboxy-2,3-dehydrobetanidin, at pH 3 indicates their generation via two possible reaction routes with two different quinonoid intermediates: dopachrome derivative and quinone methide. Both reaction paths lead to the decarboxylative dehydrogenation of betanidin. Subsequent oxidation and rearrangement of the conjugated chromophoric system results in the formation of 14,15-dehydrogenated derivatives. Betanin is oxidized with generation of a quinone methide intermediate, which rearranges to 2,3-dehydro- or neoderivatives. The products of enzymatic oxidation of betacyanins thus formed are derivatives of 5,6-dihydroxyindole and related structures known as the key intermediates in melanogenesis.