Despite its economic importance, the origin and long-term history of carob tree (Ceratonia siliqua L.) are still under debate. Since De Candolle, the wildness of Mediterranean carob populations has been questioned on the basis of paleo-botanical, archeological and philological evidence but, unfortunately, the scarce studies on the ecology and genetic diversity of wild populations have not thrown much light on this topic. The extremely low cold-stress tolerance of carob plants constituted the main argument against a long-term persistence of natural populations throughout Pleistocene in the Mediterranean. Under this scenario, the current carob Mediterranean range would be explained by human dissemination from Western Asia. However, a global phylogeographic study covering the entire distribution of carob is still lacking. We sequenced nuclear and plastid regions from both natural and cultivated populations covering the whole current distribution range of carob to explore its phylogeography based on coalescent methods and divergence time estimations. Here we report the first molecular evidence on the origin of Ceratonia siliqua and we try to set the hypothetical events that shaped the historical biogeography of this tertiary relict lineage.