A boundary between two disparate mitochondrial DNA haplotype groups exists in NCR populations from eastern Illinois. Genetically distinct strains of the Wolbachia endosymbiont were discovered on opposite sides of the NCR mtDNA border. The Wolbachia DNA sequences were obtained from insects collected some distance from the mtDNA dividing line. The putative explanation for the mtDNA divergence in NCR is a Wolbachia sweep initiated at different sites by each of the two Wolbachia strains. If the Wolbachia strains are mutually incompatible, when the two populations met a boundary would have been created that was not readily penetrated in either direction. We have begun a more detailed examination of Wolbachia ftsZ and wspA gene sequences from NCR collected close to the mtDNA boundary. Initial results indicate the presence of multiple Wolbachia sequences in some of these individuals. Some of these sequences are very similar to the sequences from the two strains previously reported. Others are quite divergent. Some possible explanations for this observation include: a) Infection of previously infected individuals at the boundary with one or more new strains of Wolbachia. Such infections could be either the result or an enabler for limited mixed infection by the two originally discovered strains. b) The new sequences are derived from recombination events occurring between the original two strains.