The monophyletic Eurasian clade of Amaryllidaceae was analyzed using plastid ndhF and rDNA ITS sequences for 33 and 29 taxa, respectively; all genera were represented by at least one species. Both maximum parsimony and Bayesian analysis were used on each data set and the combined data. Both sequence matrices resolve the Central and East Asian tribe Lycorideae as sister to the Mediterranean-centered genera of the clade, and recognize two large subclades within the greater Mediterranean region: Galantheae, consisting of Acis, Galanthus and Leucojum; and Narcisseae (Narcissus and Sternbergia)/Pancratium. However, there are areas of incongruence between the ndhF and ITS trees. When three predominantly monotypic 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, with ILD between partitions rising from P = 0.07 to 0.96. We hypothesize that lineage sorting took place after the divergence of Galantheae and Narcisseae/Pancratium from a common genepool with Hannonia, Lapiedra, and Vagaria retaining a mosaic of the ancestral haplotypes. We also performed dispersal-vicariance analysis to reconstruct biogeographic scenarios on several of the generic level phylogenies found with and without these three genera included, as well as on a species-level phylogeny of Galantheae. After the vicariant divergence of the Asian Lycorideae, North Africa and the Iberian Peninsula are the most likely areas of origin for the rest of the clade. The results of the dispersal-vicariance analysis are discussed in the context of the complex biogeographic history of the Mediterranean basin.