Technical Abstract: The relationships of the genera within the Eurasian clade of Amaryllidaceae have not been resolved previously with clarity. We analyzed plastid ndhF and rDNA ITS sequences for 33 and 29 taxa, respectively, representing all genera by at least one species, with both maximum parsimony and Bayesian analysis, alone and in combination. Both sequence matrices resolve the Central and East Asian tribe Lycorideae as sister to the Mediterranean-centered genera of the clade. Both data sets resolve two large subclades within the greater Mediterranean region: Galantheae, consisting of Acis, Galanthus and Leucojum; and Narcisseae (Narcissus and Sternbergia)/Pancratium but also have areas of incongruence when three monotypic or small genera, Hannonia, Lapiedra and Vagaria, centered in North Africa, are removed from the alignments, the two sequence matrices produce fully congruent topologies with increased support at many of the nodes. We hypothesize that lineage sorting took place after the divergence of Galantheae and Narcisseae/Pancratium from a common genepool of which Hannonia, Lapiedra and Vagaria have retained a mosaic of the ancestral haplotypes. We also use dispersal-vicariance analysis to reconstruct biogeographic scenarios on trees found with the combined matrix, and use the degree of ambiguity in the optimizations to evaluate the relative phylogenetic accuracy of the trees. The results of the dispersal-vicariance analysis are discussed in the context of the complex biogeographic history of the Mediterranean basin.