Mandragora L. (Solanaceae) is the only genus of the tribe Mandragoreae, one of the two tribes of the cosmopolitan nightshade family, which occur exclusively in Eurasia and northern Africa. The genus occurs discontinuously in the Mediterranean region, Turanian region, and on the Tibetan Plateau, representing a classical disjunction pattern in the biogeography of the Old World flora. In this study, we reconstructed the genus phylogeny using AFLP, eight plastid DNA regions and one nuclear (ITS) gene, and evaluated the taxonomic value of quantitative traits time to flowering, fruit and seed size. We also analyzed the evolutionary history of the genus based on a phylogenetic framework and dating inferred from a combined data set of seven plastid regions with one fossil calibration point. Our data suggest that Mandragora originated in the Eocene, apparently along the Tethyan coast in broadleaf deciduous mesophytic forests that covered most of the Mediterranean region at that time. The Mediterranean-Turanian Glade diverged from the Tibetan Plateau Glade about 20.5 million years ago (Ma) as a result of the plateau uplift which probably was enhanced by aridification in the interior of Eurasia. A second split within the genus occurred about 11.1 Ma and resulted in Western Mediterranean and Near East-Turanian clades. Mandragora turcomanica was found to have very closely related evolutionary history with plants from the Near East indicating a possible ancient human assisted migration from Israel to Persia in historic times. In the Tibetan Plateau area, the morphologically distinctive M. chinghaiensis is nested within the M. caulescens Glade indicating a very recent diversification within this lineage.