While pre-reproductive isolations are more and more frequently described between closely related species or within species, very little is known about their conditions of emergence. In Brazzaville, two populations (Kronenbourg and Loua) of Drosophila melanogaster show a premating isolation. Two hypotheses were proposed to explain such a situation: a local sympatric differentiation or an allopatric divergence followed by a secondary contact. A microsatellite analysis, using markers on all chromosomes, strongly suggests that the Kronenbourg population has a European origin. Therefore, the allopatric divergence between Kronenbourg and Loua populations is probably responsible for the sexual isolation observed today in sympatry, after a recent introduction of a European propagule in Brazzaville.