Phenolic compounds in apples 17 cultivars (Malus domestica Borkh.) and 3 wild forms (Malus sp.) were analyzed to study the impact of genetic background, growth site, and fruit bagging. The impact of altitude was studied in nine cultivars by analyzing fruits collected from orchards at three altitudes. Procyanidin B2 (71–628 mg/g fresh weight), (−)-epicatechin (35–357 mg/g), and chlorogenic acid (28–563 mg/g) were always the three most abundant phenolic compounds in the apple samples studied, except for the cultivar ‘Qinguan’, which had a very low content of (−)-epicatechin (13 mg/g) and procyanidin B2 (8 mg/g). The wild apples of M. prunifolia (Willd.) Borkh were 5-times richer in epicatechin (278 mg/g) and procyanidin B2 (628 mg/g) than the commercial cultivars of M. domestica Borkh (86 and 54, respectively). Among the commercial cultivars, ‘Qinguan’ had the highest level of chlorogenic acid but the lowest content of flavan-3-ols, whereas ‘Liuyuehong’ was characterized by the highest content of quercetin glycosides. Procyanidin B2, and (−)-epicatechin correlated negatively, while other phenolics positively, with altitude. The response of phenolic compounds to altitude variation depended on latitude variation and genetic backgrounds. Bagging treatment reduced the contents of most phenolic compounds, with impact of cultivars and length of re-exposure before harvest. This is also the first report on phenolic compounds in several important new cultivars, adding new knowledge on the compositional characteristics of global apple resources.