The phylogeny of the cryptic species complex of wasps in the genus Nasonia was inferred by analysis of nucleotide sequences of an rDNA internal transcribed spacer (ITS2) and the D2 region of 28S rDNA. Phylogenetic analysis showed that N. vitripennis descended from a theoretical common ancestor with that of a lineage that diverged into N. longicornis and N. giraulti. Differences in the ITS2 regions clearly distinguished two strains of N. giraulti. Another member of the Dibrachys Group, Trichomalopsis dubius, was placed outside of the Nasonia complex. The D2 region had a base substitution rate approximately 2 times slower than the ITS2 region and was used to resolve the phylogenetic affiliation of an eulophid, Melittobia digitata, to the pteromalids. Tree topology of the Nasonia complex was congruent with the phylogeny of a cluster of Wolbachia bacteria which infect these insects. The possible role of these bacteria in driving speciation is discussed.