Little is known about factors affecting anthocyanin biosynthesis in red-fleshed apples (Malus x domestica Borkh.). The objective was to establish the effects of orchard management factors on flesh anthocyanin content of dark-colored (DC) and light-colored (LC) apple clones. Flesh color was assessed by measuring color in the L, a, b mode using a spectrophotometer and predicting the anthocyanin content based on relationships between the absorption of a flesh extract at 530 nm and the L-value determined using a spectrophotometer (r2 = 0.99 ***). Fruit from the DC clone were red by 86 days after full bloom (DAFB), whereas the LC clone began to color at 136 DAFB. Color intensity in both clones decreased from the top of the tree to the base. Further, the intensity of the flesh color of the DC clone decreased with shading (94% absorption of incident photosynthetic active radiation). Covering a fruit with a UV absorbing film (100% UV absorption) had no effect on flesh color in the DC clone but decreased color in the LC clone. Fruit thinning increased color in DC and LC fruit. There was little change in flesh color during storage. However, the DC clone developed severe flesh browning as storage progressed beyond 30 days. The results demonstrated that light (visible and UV wavelength) stimulated, whereas shade inhibited, anthocyanin biosynthesis in the flesh under orchard conditions.