Fraxinus section Sciadanthus consists of three species: Fraxinus hupehensis from Central China, F. xanthoxyloides from western Himalaya, and F. dimorpha from North Africa. These species exhibit an unusual biogeographic disjunction across Central China, western Himalaya and North Africa, but the origin and evolutionary are still unclear. The phylogenetic relationships of this section are herein reconstructed using nuclear ribosomal ITS and chloroplast psbA-trnH, rpl32-trnL and matK sequence data. The Bayesian system tree constructed by ITS sequences supports the classification system proposed by Wallander , which divided Fraxinus into six sections, F. hupehensis, F. xanthoxyloides and F. dimorpha all belong to section Sciadanthus and form a sister group with section Fraxinus. We find evidence that F. xanthoxyloides may have originated from hybridization between F. dimorpha and a Eurasian species. The divergence time suggests that Fraxinus first differentiated at 42.05 Ma, section Sciadanthus initially diverged at 21.86 Ma, and F. hupehensis diverged at 11.87 Ma. Vicariance driven by the uplifts of the Tibetan Plateau in the Tertiary may be the main reason for the formation of the disjunct distribution in section Sciadanthus. F. hupehensis and F. xanthoxyloides may be relict plants influenced by this process.