In this study, we report data about the presence of Wolbachia in Drosophila yakuba, D. teissieri, and D. santomea. Wolbachia strains were characterized using their wsp gene sequence and cytoplasmic incompatibility assays. All three species were found infected with Wolbachia bacteria closely related to the w Au strain, found so far in D. simulans natural populations, and were unable to induce cytoplasmic incompatibility. We injected w Ri, a CI-inducing strain naturally infecting D. simulans, into the three species and the established transinfected lines exhibited high levels of CI, suggesting that absence of CI expression is a property of the Wolbachia strain naturally present or that CI is specifically repressed by the host. We also tested the relationship between the natural infection and w Ri and found that it fully rescues the w Ri modification. This result was unexpected, considering the significant evolutionary divergence between the two Wolbachia strains.