The intracellular bacterium Wolbachia invades arthropod host populations through various mechanisms, the most common of which being cytoplasmic incompatibility (CI). CI involves elevated embryo mortality when infected males mate with uninfected females or females infected with different, incompatible Wolbachia strains. The present study focuses on this phenomenon in two Drosophila species: D. simulans and D. sechellia. Drosophila simulans populations are infected by several Wolbachia strains, including wHa and wNo. Drosophila sechellia is infected by only two Wolbachia: wSh and wSn. In both Drosophila species, double infections with Wolbachia are found. As indicated by several molecular markers, wHa is closely related to wSh, and wNo to wSn. Furthermore, the double infections in the two host species are associated with closely related mitochondrial haplotypes, namely siI (associated with wHa and wNo in D. simulans) and se (associated with wSh and wSn in D. sechellia). To test the theoretical prediction that Wolbachia compatibility types can diverge rapidly, we injected wSh and wSn into D. simulans, to compare their CI properties to those of their sister strains wHa and wNo, respectively, in the same host genetic background. We found that within each pair of sister strains CI levels were similar and that sister strains were fully compatible. We conclude that the short period for which the Wolbachia sister strains have been evolving separated from each other was not sufficient for their CI properties to diverge significantly.