Due to its economic value and evolutionary importance among monocots and Dioscoreales, Dioscorea has been extensively studied phylogenetically. All analyses have produced congruent results resolving ten consistent main clades but were based solely on plastid data. Here we present the first phylogenetic tree of Dioscorea based on a lowcopy nuclear gene, xanthine dehydrogenase (Xdh). The Xdh topology and the divergence order of the main Dioscorea clades are congruent with those of the plastid-based trees, showing an early diverging position of Stenophora, followed by those of the two New World clades (NW I, NW II) and a still unresolved relationship between the African and Mediterranean clades plus D. tentaculigera. Subsequent branches include a more recently evolved clade B of Dioscorea comprising all cultivated species, the well-supported Malagasy, compound-leaved (CL) and Rajania clades and a clade composed of mixed Birmanica and Enantiophyllum accessions. We also identified a more recently evolved New World clade (NW III), represented by D. anomala, nested in clade B.