In reconstructing taxon evolution, historical biogeography is concerned with two kinds of speciation events, both resulting in a fragmented taxon distribution - vicariance and dispersal. We used PCR-RFLP of plastid DNA and a ribosomal internal transcribed spacer, sequencing of the rps16-trnK chloroplast region, flow cytometry (florescence-activated cell sorter; FACS), and ecological niche modeling to understand the role of these two processes in a disjunct distribution of genus Mandragora. The observed phylogeographic structure only partly coincided with currently recognized species. Commonly used recognition of a single species in the whole Mediterranean is not supported, given that a single haplotype observed from Morocco and Spain to Turkey is strikingly different from the haplotypes found in Israel. In the Sino-Himalayan area, the previously recognized M. chinghaiensis is nested within the M. caulescens clade indicating a very recent diversification within this lineage. And, most importantly, the obtained minimum spanning tree, observed haplotype distribution, and results of FACS call into question the existence of M. turkomanica as a species, and even as a lower taxonomic unit. Rather, the mandrake from Central Asia is nested within those from Israel, suggesting their closely related evolutionary history and ancient human assisted migration from Israel to Persia in historic times. Our study suggests that human assisted migration can explain the cases of disjunct species distribution for which vicariance was previously considered as the only plausible explanation.