Wolbachia are endosymbiotic bacteria that may alter the reproductive mechanisms of arthropod hosts. Eusocial termites provide considerable scope for Wolbachia studies owing to their ancient origin, their great diversity and their considerable ecological, biological and behavioral plasticity. This article describes the phylogenetic distribution of Wolbachia infecting termites of the Cubitermes genus, which are particularly abundant soil-feeders in equatorial Africa. Fourteen colonies of the Cubitermes sp. affinis subarquatus complex of species were screened using five bacterial genes (wsp, ftsZ, coxA, fbpA and 16S rRNA genes) and a striking diversity of Wolbachia strains was identified within these closely related species. In the host complex, three Wolbachia variants were found that were not in the super groups usually reported for termites (F and H), each infecting one or two Cubitermes species.