The biogeography of the date palm (Phoenix dactylifera L.), the origin, structure and dynamics of its agrobiodiversity, and the relationships to other species of Phoenix are reviewed. Phoenix dactylifera is confirmed as a distinct species and has closest affinities with P. sylvestris and P. atlantica. Multiple origins of domestication are likely, within two highly distinct primary gene pools, one oriental (Middle East) and one occidental (south-western Europe and north-western Africa), subsequently partially admixed, especially in the intermediate zone of North Africa. A rationale to identify wild populations of P. dactylifera, using a combination of chloroplast barcoding and nuclear microsatellite genotyping is proposed. A domestication model is presented and the domestication syndrome is described, as well as the nature of cultivars. All data indicate a strong geographic structure of the genetic diversity of the date palm at all scales (local, regional, global), and the importance of both isolation and intraspecific gene flow in shaping the present day agrobiodiversity, while there is no evidence of interspecific hybridization in the cultivated gene pool.