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The pitahaya (Hylocereus spp.) is a cactus native to America. Despite the great diversity of species located in Mexico, there are few studies on the nutritional and nutraceutical value of its exotic fruits, ancestrally consumed in the Mayan culture. An evaluation was made regarding the physical-chemical characteristics, the nutritional components and the antioxidants of the fruits of H. ocamponis (mesocarp or red pulp) and H. undatus (white pulp), species of great commercial importance. The pulp of the fruits presented nutritional and nutraceutical differences between both species. The red pulp of H. ocamponis presented the highest content of betalains (15.94 mg 100 g-1), ascorbic acid (10.13 AAE mg 100 g-1) and antioxidant activity (2009.58 μM TE 100 g-1) compared to that of H. undatus. The seeds of both species had a higher content of linoleic acid (ω-6) compared to other fatty acids. The underused skin (epicarp) of the white pulp pitahaya presented a higher content of betalains (19.83 mg 100 g-1) than that found in the pulp and the red skin of the other species (13.21 mg 100 g-1). The red pitahaya that is for regional consumption presented a better functional quality. The skin of both species could be a source of pigments in the food industry.