Using portions of three mitochondrial genes to resolve the uncertain systematic relationships, we constructed a phylogeny of the “gray shrikes” in the genus Lanius. We used the tree and estimates of the rate of evolution of passeriform mtDNA genes to project the nodes' ages and to assess the pattern and age of egg-rejection behavior in shrikes. Our results suggest that Lanius excubitor and L. m. meridionalis are sister taxa and that this clade is sister to L. ludovicianus, then L. sphenocercus is sister to this clade. Lanius excubitor from the Old World was considerably diverged from both New World species and part of a clade also containing four other subspecies of L. meridionalis. The paraphyly and sequence divergence between New World and Old World L. excubitor suggest that these populations represent distinct species. Mapping egg rejection onto the phylogeny suggests that rejection is deeply rooted in shrikes, as it is present as deep as two species, L. collurio and L. bucephalus, that are outgroups to the gray shrikes and in the derived L. ludovicianus. Rejection in L. ludovicianus may have been retained as long as 1.1–1.8 million years, since its clade split from the Old World L. sphenocercus, providing more evidence that once hosts evolve rejection they retain it for long periods of time. These results suggest hosts are becoming increasingly resistant to brood parasitism, which will force parasites to specialize on a few host species.