A molecular phylogeny is presented for the five main species of Aphthona flea beetles that were introduced to North America in conjunction with the leafy spurge (Euphorbia esula L.) biological control program. The mitochondrial genome was examined using polymerase chain reaction-restriction fragment length polymorphism (RFLP) of a 9,000-bp segment and nucleotide sequencing of a 575-bp piece of cox1-cox2. A neighbor—joining tree of the RFLP data, along with neighbor-joining and maximum parsimony trees of the sequence alignments, all had the same major branching pattern. Each of the recognized species was a well defined clade. Three within species subbranches had very limited mitochondrial DNA diversity. One was a Wolbachia-infected lineage of A. nigriscutis most likely generated by a Wolbachia sweep where the spreading Wolbachia infection brought along the infected mitochondrial haplotype. Two of three subclades of A. lacertosa also had very little genetic diversity. One of these subclades also displayed a divergence from the other two that was analogous to the divergence observed between some of the other species pairs, suggesting it may be a cryptic species. Its distribution was restricted to Canada. The other genetically depauperate A. lacertosa line was the only lineage recovered in the United States. The geographically restricted nature of some of the genetic lines could be exploited to possibly improve biological control in some habitats through redistribution to other locations. It is not obvious that either Wolbachia infection or a narrow genetic base has had any detrimental effect on biological control.