Phytochemical composition and antioxidant activity of eight apple (Malus domestica) cultivars (Casa Nova, Fuji, Golden Delicious, Granny Smith, Jonagored, Reinette Grise, Royal Gala, and Starking) from the MacA de Alcobaca protected geographic indication, Portugal, were characterized to support market segmentation based on phytochemical content. Total phenolics, flavonoids, and anthocyanin contents, individual polyphenols and antioxidant activity were assessed in the flesh and skin of fruit at the ripe stage. A market segmentation of apple cultivars based on these bioactive phytochemicals is proposed. Fruit eaten with the peel can be segmented in three classes: (1) the flavonoid-rich Starking, Reineta, Galaxy, Casa Nova, Jonagored; (2) the quercetin-rich Fuji, Galaxy, Casa Nova; and (3) flavonol and procyanidin-rich Starking, Reinette, Jonagored, Casa Nova. When apples were peeled before consumption, two phytochemical classes were proposed: (1) the flavonoid-rich Reinette and Casa Nova, and the (2) chlorogenic acid-rich Reineta, Casa Nova, and Starking.