Cotesia sesamiae (Cameron) (Hymenoptera: Braconidae) is an indigenous, gregarious, larval endo/parasitoid which is widely distributed in Africa and attacks mid- to late instars of stemborers. There is renewed interest in using Co. sesamiae for biological control to reduce the problems caused by stemborers. However, Wolbachia sp., a bacterial symbiont of some populations of Co. sesamiae, poses some threat to the successful use of the parasitoid for stemborer control. This bacterium's common effect is cytoplasmic incompatibility between infected males and uninfected females. Polymerase chain reaction (PCR) tests were carried out on parasitoid samples collected from 5 locations in Kenya and 8 other countries in eastern Africa. Wolbachia presence was detected in Co. sesamiae populations from Coast and Machakos in Kenya, and from samples collected from 6 other eastern and southern African countries. No infection was detected from western Kenya, Uganda and Malawi. Cross mating among 3 infected populations (North Coast, South Coast and Machakos) and 2 uninfected populations (Kitale and Kuja) was done to establish which populations were reproductively compatible. Biological parameters, such as brood size and percent females were compared among the different crosses. One-way incompatibility, indicative of Wolbachia infection, was observed from the crosses between males of either Mombasa or Machakos arid females from Kitale. Selection of compatible Co. sesamiae populations is critical to successful augmentation biological control programmes.