The presence and distribution of the intracellular bacteria Wolbachia in the arthropod subphylum Chelicerata (including class Arachnida) has not been extensively explored. Here we report the discovery of Wolbachia in scorpions. Five strains found in host species of the genus Opistophthalmus (Southern African burrowing scorpions) have been characterized by Multilocus Sequence Typing and by Wolbachia Surface Protein. Phylogenetic analyses indicate clustering in the supergroup F and a high genetic relatedness among all scorpion strains as a result of a potential transmission within the host genus. The F-group is an uncommon lineage compared to the A and B supergroups, although it is present in a broad range of hosts (including insects, filarial nematodes, and now arachnids) and across a large geographical area (e.g., North America, Africa, Europe, and Australia). It also shows no evidence of recombination and has a significantly higher genetic diversity than supergroup A and B. Overall, this pattern suggests an older radiation of F-strains with respect to A and B-strains, followed by limited horizontal transmission across host genera and reduced genetic flux among strains. A more extensive sampling of supergroup F-strains is required to confirm this scenario.