Corn seeds contain natural pigments and antioxidants, such as the molecular variants of flavonoids and carotenoids. The aleurone and pericarp tissues from pigmented genotypes were extracted for metabolic fingerprinting and evaluated using UV-vis and mass spectrometry (MS). MS ionomic fingerprints classified samples according to genetic background and kernel color. The MS/MS fragmentation pattern (Daughter and Neutral Loss methods) allowed the tentative identification of 18 anthocyanins with glycosyl, malonyl, and succinyl moieties, including 535 / for cyanidin-3--(6″-malonyl-glucoside) and 621 / for cyanidin-3--(3″,6″-dimalonyl-glucoside). We also detected 663 / for pelargonidin-3--(disuccinyl-glucoside) and 633 / for peonidin-3--(disuccinyl-glucoside). Cyanidin-based anthocyanins were the most abundant in dark purple colored kernels, while pelargonidins predominated in the red-pink kernels of the "" landrace. Grains of "" had a simultaneous pigmentation of aleurone and pericarp, while Vitamaize had purple pigmentation only in the aleurone layer. Most landraces had a white endosperm, while Vitamaize had a yellow endosperm and a dark seed coat. We conclude that Vitamaize grains contain both carotenes and anthocyanins, and therefore it is proposed as a nontransgenic agronomically improved variety of tropical purple maize, a good source for organic superfoods.