Although sexual isolation is one of the most important causes of speciation, its genetic basis is largely unknown. Here evidence is presented that suggests that sexual isolation between two closely related species of Drosophila is largely caused by differences in female cuticular hydrocarbons. This difference maps to only one of the three major chromosomes, implying that reproductive isolation might have a fairly simple genetic basis. The effect of the hydrocarbons on courtship may help explain the ubiquitous asymmetry of sexual isolation between many pairs of Drosophila species.