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 under-sampled host species. Here, we report on the putative discovery of a new genetic lineage, denoted super group H, which infects the Isopteran species Zootermopsis angusticollis and Z. nevadensis. Evidence for this novel super group 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 super group and validate the positioning of the other Wolbachia super groups. This discovery is the first example of a termite Wolbachia that is highly divergent from the Isopteran Wolbachia previously described in super group F. This study highlights the importance of multilocus approaches to resolving Wolbachia super group relationships. It also suggests that surveys of Wolbachia in more earlier-originating (and under-sampled) groups of arthropods are more apt to reveal novel genetic diversity.