In order to contribute more to human health, revealing the nutritional potential of fruit germplasm sources that have rich phytochemical compounds has gained importance today and has become one of the breeding objectives of various fruit species. Many nutritional components of wild apples have been considered as useful sources for apple breeding efforts, but studies on the phytochemical compounds of native apple genetic resources grown in local areas are limited. This study was carried out to investigate the phytochemical compounds of 19 native apple genotypes grown in Giresun in the eastern Black Sea region of Turkey and to compare them with those of three commercial varieties ('Granny Smith', 'Fuji', and 'Royal Gala'). The total phenolic contents of the genotypes ranged from 141.7 mg per 100 g (Yesilsut) to 1036.8 mg per 100 g (Cipir). Antioxidant activity was determined to be between 505.6 mu mol per 100 g (Ahmet) and 5041.8 mu mol per 100 g (Cipir). The total flavonoids ranged between 11.2 mg per 100 g (Beyaz) and 95.3 mg per 100 g (Maden). Uzun had the highest content of malic acid (15.33 g l(-1)) and tartaric acid (1.008 g l(-1)). The highest values for succinic acid and oxalic acid were detected in Cipir (1.192 g l(-1) and 0.484 g l(-1), respectively). Most of the native apple genotypes had higher levels of phytochemical compounds than those of standard apple cultivars. Principal component analysis showed that the phytochemical components could effectively explain the variability among the native apple genotypes, which exhibited wide variation in terms of phytochemical compounds. Most genotypes contained higher levels of phytochemical compounds than standard apple cultivars. The data imply that the native apple genotypes are an important source of phytochemical compounds and that native apple genotypes with higher contents of bioactive compounds can be used as genetic material for apple breeding programs. They might contribute to the development of new apple cultivars with enhanced health benefits.