This study reports the genetic diversity among Chilean heritage blood-flesh peaches and the characterization of phytochemicals and bioactive compounds present in these fruits. A genetic diversity analysis using 7,934 SNP markers was performed. The average observed heterozygosity (Ho=0.09) was very low in the 75 Chilean blood-flesh peach trees, whereas 14 commercial peach varieties had significantly higher levels of heterozygosity (Ho=0.32). Furthermore, the blood-flesh peach lines were genetically similar, and all of these lines were genetically different from the commercial varieties. A comparative analysis was carried out between the epicarp and mesocarp of the peach fruits. Fruit quality parameters were evaluated at harvest (weight, size, firmness and soluble solids), and concentrations of total polyphenols, anthocyanins, carotenoids, as were macro (P, K, Ca, Mg) and microelements (Fe, Zn, Mn, B, Cu). These analyses showed that blood-flesh peaches have high concentrations of anthocyanins (cyanidin-3-glucoside (C3G) and cyanidin-3-rutinoside (C3R)) when compared to commercial varieties with white or yellow mesocarps. A comparison was performed among Chinese, French and Chilean varieties, with similar values found for the antioxidant compounds. No significant differences in the microand macroelement contents were detected in these blood-flesh fruits compared to commercial varieties.