Nasonia consists of three closely related species of parasitoid wasps that are all infected with the endosymbiotic bacteria Wolbachia, a reproductive parasite common in arthropods. This situation presents the opportunity to compare patterns of variation in three associated genomes, Wolbachia and the nuclear and mitochondrial genomes of its host. Furthermore, although Nasonia wasps are emerging as a model for evolutionary and genetic studies, little is known about their genetic variability. Using amplified fragment length polymorphisms (AFLPs), all three species present a relatively high level of nuclear polymorphism and have different patterns of variation, with one of the species, Nasonia giraulti, being divided into two divergent subgroups. In each species, the mitochondrial pattern of variation is different from the nuclear pattern, possibly due to genetic hitchhiking of the mitochondria during (cytoplasmically inherited) Wolbachia sweeps. Mitochondria in Nasonia show a synonymous substitution rate approximately 10-15-fold higher than nuclear genes, probably reflecting an elevated mitochondrial mutation rate that is among the highest found in insects. Finally, all three species are doubly infected with their own strains of Wolbachia, one each from the two major supergroups (A and B). Sequence analysis reveals that each of the three Nasonia species acquired their A and B bacteria independently by horizontal transfer events from other insects with the exception of B type Wolbachia in N. longicornis and N. giraulti, which were acquired prior to speciation and then codiverged with the host. This represents one of the few clear-cut examples of codivergence of Wolbachia during host speciation.