We conducted classical genetic analysis of the difference in male genitalia and hybrid sterility between the island-dwelling sibling species Drosophila sechellia and D. mauritiana. At least two loci (one on each autosome) are responsible for the genital difference, with the X chromosome having no significant effect. In contrast, male hybrid sterility is caused by at least four gene loci distributed among all major chromosomes, with those on the X chromosome having the largest effect. We also show that the large difference in ovariole number between D. sechellia and its mainland relative D. simulans is due to at least two gene substitutions, one on each major autosome. The X and the left arm of the second chromosome, however, have no significant effect on the character. This implies that the evolution of reduced ovariole number involved relatively few gene substitutions. These results extend previous findings that morphological differences between Drosophila species are caused by genes distributed among all chromosomes, while hybrid sterility and inviability are due primarily to X-linked genes. Because strong X-effects on male sterility have been found in all three pairwise hybridizations among D. simulans, D. sechellia and D. mauritiana, these effects must have evolved at least twice independently.