The provenance of white sharks (Carcharodon carcharias) in the Mediterranean is both a conundrum and an important conservation issue. Considering this species's propensity for natal philopatry, any evidence that the Mediterranean stock has little or no contemporary immigration from the Atlantic would suggest that it is extraordinarily vulnerable. To address this issue we sequenced the mitochondrial control region of four rare Mediterranean white sharks. Unexpectedly, the juvenile sequences were identical although collected at different locations and times, showing little genetic differentiation from Indo-Pacific lineages, but strong separation from geographically closer Atlantic/western Indian Ocean haplotypes. Historical long-distance dispersal (probably a consequence of navigational error during past climatic oscillations) and potential founder effects are invoked to explain the anomalous relationships of this isolated 'sink' population, highlighting the present vulnerability of its nursery grounds.