The intracellular bacteria, Wolbachia, are well known for inducing reproductive alterations in arthropod hosts, especially insects. The ancient origin and huge diversity, combined with the ecological, biological and behavioral plasticity of termites, make the latter exciting candidates for studying the interactions of Wolbachia. In the present study, we investigated the distribution of Wolbachia in populations of Odontotermes spp. and Coptotermes heimi termites occurring in 14 colonies (12 Odontotermes spp. and two C. heimi) from different locations in India. A striking diversity was observed among Wolbachia strains in closely related hosts based on five MLST genes (ftsZ, coxA, fbpA, hcpA and gatB) and the 16S rRNA gene. Wolbachia variants from two supergroups (B and F) were found in both the termite genera under study. This is the first report of Wolbachia infection in the Odontotermes genus. Although F Wolbachia supergroup infection is already reported in Coptotermes lacteus and Coptotermes acinaciformis, in this study, the two C. heimi species exhibited infection by two distinctly different Wolbachia supergroups (B and F).