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Bacteria in the genus Wolbachia are widespread in arthropods and can induce sex-ratio distortion or cytoplasmic incompatibility in their hosts. The phylogeny of Wolbachia has been studied using 16S rDNA and the cell cycle gene ftsZ, but sequence variation of those genes is limited. The spacer 2 region (SR2) was amplified to determine whether this region would improve phylogenetic resolution. The SR2 of Wolbachia is 66 bp long, shows higher variation than ftsZ and has very low homology with closely related bacteria. Due to the small length of SR2 of Wolbachia, little phylogenetic information could be retrieved.