Sometimes the source of fruit flies fails to be found if there is no fruit sitting on your countertop. One overlooked source is sink drains and garbage disposals. They can feed and breed on the gooey residue inside.
Use the old baking soda and vinegar trick on your drain! Pour about 1/4 cup baking soda into your drain or disposal followed by a few glugs of plain ole white vinegar. Let it sizzle and stew for a few minutes then flush with hot water. This will not only get rid of the fruit flies and goo but will sanitze and deodorize your drain. This will even clear up slow drains or small clogs without the use of harsh chemicals! :-)