Old English fleoge "fly, winged insect," from Proto-Germanic *fleugjon (cf. Old Saxon fleiga, Old Norse fluga, Middle Dutch vlieghe, Dutch vlieg, Old High German flioga, German Fliege "fly); literally "the flying (insect)" (cf. Old English fleogende "flying"), from same source as fly (v.1).
Originally any winged insect (hence butterfly, etc.); long used by farmers and gardeners for any insect parasite. The Old English plural in -n (cf. oxen) gradually normalized 13c.-15c. to -s. Fly on the wall "unseen observer" first recorded 1881. An Old English word for "curtain" was fleonet "fly-net." Fly-swatter first attested 1917. Fly-fishing is from 1650s.