A better understanding of the evolutionary relationship between modern humans and Neanderthals is essential for improving the resolution of hominin phylogenetic hypotheses. Currently, four distinct chronologies for the timing of population divergence are available, ranging from the late Middle Pleistocene to the late Early Pleistocene, each based on different interpretations of hominin taxonomy. Genetic data can present an independent estimate of the evolutionary timescale involved, making it possible to distinguish between these competing models of hominin evolution. We analysed five dated Neanderthal mitochondrial genomes, together with those of 54 modern humans, and inferred a genetic chronology using multiple age calibrations. Our mean date estimates are consistent with a process of genetic divergence within an ancestral population, commencing approximately 410-440 ka. These results suggest that a reappraisal of key elements in the Pleistocene hominin fossil record may now be required.