Drosophila santomea and Drosophila yakuba are two sister species inhabiting Saõ Tomé island. Previous studies showed that both species display strong reproductive isolation, although they can produce a few viable hybrids. Our study tried to understand the mechanism of this ethological isolation between two allopatric strains. A strong sexual isolation was confirmed, with a marked asymmetry. Comparisons of latency times to either courtship or copulation suggest that males do not discriminate females, whereas D. yakuba females, but not D. santomea females, accept their homospecifics more quickly. Cuticular hydrocarbon compositions of both species and sexes were also established with gas chromatography (GC) and GC/mass spectrometry analysis. All have (Z)-7-tricosene as their major compound. There are several quantitative differences between species for few minor compounds. The largest difference concerns n-heneicosane, which is more abundant in D. santomea than in D. yakuba flies (up to seven times more between males). A similar quantitative difference was also found in a pair of sympatric strains. Furthermore, D. yakuba males artificially perfumed with n-heneicosane were discriminated negatively by D. yakuba females, suggesting a role for this compound in the sexual isolation between these two species.