Fruit flies (or Drosophila melanogaster) are stealthy little guys that seem to smell rotting fruit from miles away. They do not come from the inside. If you're wondering where fruit flies come from, you're probably not going to love this answer. early fall because it's the harvest season, and America is filled with the fruits of the earth. You Asked: Are Cleanses Healthy? Fruit flies come from the up to eggs adults lay. That stuff can be ripened fruits or vegetables, as well as drains, garbage disposals, empty Missing: fattening.