Cotesia sesamiae (Hymenoptera: Braconidae) is an indigenous, gregarious, larval endoparasitoid that attacks mid- to late-instar of the stem borer larvae. Although the parasitoid is distributed widely throughout Africa, not all local populations appear to be equally effective in controlling stem borers. Consequently, there is an interest in releasing the more effective strains in areas that already have very low populations of C. sesamiae. Some C. sesamiae populations are infected with bacterial symbionts in the genus Wolbachia, which may induce cytoplasmic incompatibility. Using an antibiotic treatment, we have established that the Wolbachia infection causes cytoplasmic incompatibility of the female mortality type in C. sesamiae. Using a simple recurrent equation model, we showed that mixing infected and uninfected populations that exhibit cytoplasmic incompatibility causes a transient, but possibly long, reduction in population growth rate. Knowledge of the infection status of native populations and populations that would be introduced could be used to avoid the incompatibility problems, by adjusting the population that will be introduced to the infection status of the native population.