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Taxonomy See also list of flies. Apple maggot, (Rhagoletis pomonella), species of fruit fly that is a serious apple pest in North America. The adult female lays its eggs beneath the skin of apples, leaving pits and dimples on the fruit. The larvae then tunnel through the flesh, causing it to become spongy, discolored, and prone to internal decay. The resulting damage reduces the marketability of the affected apples and causes fruit loss. Some populations of the...