Answer: The cherry fruit fly is responsible for worms (more precisely, maggots) in the fruit. The worms exit the fruit when they're mature (so you'll see exit holes). Then they pupate in the soil before becoming adults. When adults emerge, they lay eggs just beneath the skin of the developing cherries. The only way to tell for sure if your cherries have worms is to inspect each one, cutting it open or at least looking for holes in the skin.
These pests can remain in the soil for up to three years so practicing good garden sanitation is a giant step in keeping them under control. Rake and remove all fallen leaves and fruit at the end of the season to keep infested fruit away from the tree. If you place weed barrier over the soil beneath the tree and cover it with decorative bark, you will inhibit the worm's ability to pupate in the soil.
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