Wolbachia are one of the most abundant groups of bacterial endosymbionts in the biosphere. Interest in these heritable microbes has expanded with the discovery of wider genetic diversity in undersampled host species. Here, we report on the putative discovery of a new genetic lineage, denoted supergroup H, which infects the Isopteran species Zootermopsis angusticollis and Z. nevadensis. Evidence for this novel supergroup is based on portions of new Wolbachia gene sequences from each species spanning 3.5 kilobases of DNA and the following genes: 16S rDNA, dnaA, gltA, groEL, and ftsZ. Single-gene and concatenated maximum likelihood phylogenies establish this new supergroup and validate the positioning of the other Wolbachia supergroups. This discovery is the first example of a termite Wolbachia that is highly divergent from the Isopteran Wolbachia previously described in supergroup F. This study highlights the importance of multilocus approaches to resolving Wolbachia supergroup relationships. It also suggests that surveys of Wolbachia in more earlier-originating (and undersampled) groups of arthropods are more apt to reveal novel genetic diversity.