Host plant associated genetic differentiation is a common phenomenon in phytophagous insects, but the degree to which such associations sequentially drive diversification at higher trophic levels is not as well understood. A recent study examining neutral molecular markers in Hyalopterus aphids revealed that genetic structure in this genus is strongly determined by primary host plant use (Prunus spp.). In this paper, we take a similar approach to determine whether this host plant specificity has affected genetic structure in the parasitoid Aphidius transcaspicus, an important natural enemy of Hyalopterus spp. in the Mediterranean. Mitochondrial DNA (428 bp) and seven microsatellite loci were examined in parasitoids collected from aphid populations on almond, apricot, peach and plum trees from Spain and Greece. In contrast to the previous findings for Hyalopterus from the same regions, here we find no evidence for host associated diversification in A. transcaspicus at the species level or below, though geographic structure between regional populations is exceptionally high. These findings have several implications for our understanding of the ecology and evolution of A. transcaspicus as well as for its use as a biological control agent for Hyalopterus, suggesting that a consideration of host plant specificity may be less critical than factors such as climatic suitability or geographic origins of invasive populations.