Among the most destructive enemies of the apple orchard are the codling moth, various species of mites, the woolly aphid, the apple maggot, the red-banded leaf roller, and scale insects. Field mice, which nibble on the tree's bark, are also destructive. Bacteria cause diseases, such as fireblight. The fungus growths that cause apple rust, apple scab, and mildew are also very damaging.

Various pesticides are used to control crop damage. Disease-resistant varieties of trees have been developed.

The Asian apple from which all common apple varieties are derived is Malus pumila of the rose family, Rosaceae.