Antioxidant capacity and contents of total phenolics, anthocyanins, flavonoids, and vitamin C were evaluated in 218 genotypes from 15 peach and nectarine breeding progenies. Significant differences were found among progenies on the fruit antioxidant profile, corroborated by the high contribution showed by cross to the phenotypic variance of each phytochemical trait analyzed (16-45%). Phytochemical profile varied depending on peach/nectarine and yellow/white flesh color qualitative traits. On the other hand, no significant effect of year was found on the bioactive profile of peaches and nectarines. Antioxidant capacity was linearly correlated to total phenolic content, but correlation varied depending on the progeny. No correlation was found for vitamin C versus any other phytochemical trait. The results suggest the importance of genetic background on the antioxidant profile of peaches and nectarines and stress its relevance for the ultimate objective of this work: selecting new peach and nectarine genotypes rich in bioactive compounds to benefit consumer's health.