Cherry fruit is a natural food that has been consumed since ancient times due to its remarkable nutritional and therapeutic properties. In this study, total phenolic, total flavonoid, total monomeric anthocyanin contents, total antioxidant capacity and polyphenolic contents of fruit samples belonging to 14 (two of them endemic) different Prunus (cherry) taxa naturally distributed in Turkey were compared. Qualitative and quantitative determination of 23 individual phenolic compounds (fourteen phenolic acids, five flavonols, one flavan-3-ol, one flavone, one dihydrochalcone and one phytoalexin) was performed by LC–MS/MS (liquid chromatography technique coupled with tandem mass spectrometry). Antioxidant activities of fruit samples were determined using CERAC, CUPRAC and ABTS test methods. According to the results obtained, it was found that Prunus mahaleb var. alpina (107.57 mg cyanidin 3-glucoside/100 g FW) and Prunus mahaleb var. mahaleb (90.95 mg cyanidin 3-glucoside/100 g FW) had higher anthocyanin content compared to other fruit samples. It was determined that Prunus incana var. velutina, one of the endemic species, has a remarkable total phenolic content (10.76 mg gallic acid/g FW), individual phenolic content (641.58 mg/ 100 g, a total of individual phenolics with LC–MS/MS) and total antioxidant capacity (25.1 mg Trolox/100 g FW with CERAC assay). This article is the first study to report the comparative phytochemical content of different Prunus taxa in Turkey and the phytochemical properties of Prunus incana var. velutina. It has been concluded that endemic Prunus incana var. velutina has the potential to be used as an alternative to the taxa Prunus mahaleb, Prunus avium and Prunus vulgaris as a health-protective food and as a food additive due to its remarkable polyphenolic content, anthocyanin content and total antioxidant capacity.