Pitaya is a tropical fruit from a newly cultivated plant in Turkey that has increasing economic value. In this study, its seed properties were investigated. Pitaya fruit samples used in the research were obtained from local producers in the Gazipaşa/Antalya region. The dry matter, protein, oil, and ash content of H. polyrhizus and H. undatus pitaya seeds were 89.7% to 89.1%, 19.8% to 17.5%, 22.8% to 24.0%, and 2.8% to 4.09%, respectively. The oil and protein contents of the seeds were very high. The total phenolic content, α-tocopherol content, γ-tocopherol content, free radical scavenging activity, and induction time of H. polyrhizus and H. undatus pitaya seeds were 12.8 to 11.9 mg GAE/g dry sample, 3.67 to 2.75 g/kg oil, 1.29, 1.64 g/kg oil, 46.9% to 51.5%, and 5.37 to 5.07 h, respectively. Seeds contained significant amounts of phenolic compounds and tocopherols, which play an important role in increasing oxidative stability. The percent inhibition of DPPH indicated that pitaya seeds may be evaluated as an antioxidant source. Unsaturated fatty acids were high in seed oils of both pitaya species. Linoleic acid, a polyunsaturated fatty acid, was dominant in both pitaya species. The chemical properties of the seeds were similar to those of species grown in tropical countries. Future studies should investigate other pitaya species grown in Turkey.