Sexual isolation between the sibling species D. simulans and D. mauritiana is due largely to the rejection of D. simulans males by D. mauritiana females. Genetic analysis shows that genes on the X and third chromosomes contribute to the differences between males causing sexual isolation, while the Y chromosome, second chromosome and cytoplasm have no effect. These chromosome effects differ from those observed in a previous analysis of sexual isolation in hybrid females, implying that different genes cause sexual isolation in the two sexes.