Pitaya fruits (Stenocereus spp.) contain betalains and phenolic compounds that have not been completely characterized. Fruits of two ecotypes of S. pruinosus, red-fleshed (SpR) and orange-fleshed (SpO), and two of S. stellatus, red-fleshed (SsR) and white-fleshed (SsW), were characterized in their betalains and phenolic compounds. The chromatographic profile of betalains was similar in SpR, SpO, and SsR, where indicaxanthin, gomphrenin I, phyllocacthin, and their isomers predominated. Betaxanthins content was higher than betacyanins and ranged from 17,706.7±1128.1 to 22,053.6±328.1µg/g dry sample. The identified phenolics mostly corresponded to hydroxycinnamoyl derivatives, flavonols and flavanones. The phenolics content was higher in S. stellatus than in S. pruinosus. The ecotype SsW, that had flesh without color, showed the highest concentration. The antioxidant capacity varied within 9.21±0.84 and 2.41±0.36μmolTrolox/g fresh sample, as determined by the ABTS assay. By its phytochemical composition, the fruits of pitaya can be a good source of antioxidant compounds.