Dating of population divergence is critical in understanding speciation and in evaluating the evolutionary significance of genetic lineages, upon which identification of conservation and management units should be based. In this study we used a multilocus approach and the Isolation-Migration model based on coalescence theory to estimate the time of divergence of the Spanish and Eastern imperial eagle sister species. This model enables estimation of population sizes at split, and inference of gene flow after divergence.Our results indicate that divergence may have occurred during the Holocene or the late Pleistocene, much more recently than previously suspected. They also suggest a large population reduction at split, with an estimated effective population size several times smaller for the western population than for the eastern population. Asymmetrical gene flow after divergence, from the Eastern imperial eagle to the Spanish imperial eagle, was detected for the nuclear genome but not the mitochondrial genome. Male-mediated gene flow after divergence may explain this result, and the previously reported lower mitochondrial diversity but similar nuclear diversity in Spanish imperial eagles compared to the Eastern species.Spanish and Eastern imperial eagles split from a common ancestor much more recently than previously thought, and asymmetrical gene flow occurred after divergence. Revision of the phylogenetic proximity of both species is warranted, with implications for conservation.