Fraxinus section Sciadanthus is known with 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， whereas their origin and evolutionary remain unclear. The phylogenetic relationships of this section was investigated using nuclear ribosomal ITS and chloroplast genes psbA-trnH， rpl32-trnL and matK. The Bayesian system tree constructed by ITS sequences supports the classification system proposed by Wallander， in which the species of Fraxinus were classified into six sections. F. hupehensis， F. xanthoxyloides and F. dimorpha were all resided to section Sciadanthus and formed a sister group with section Fraxinus. We found that F. xanthoxyloides may have originated from hybridization between F. dimorpha and a Eurasian species. The divergence time suggested that Fraxinus first differentiated at 42.05 Ma， section Sciadanthus initially diverged at 21.86 Ma， and F. hupehensis diverged at 11.87 Ma. The uplifts of the Tibetan Plateau in the Tertiary may be the driving force and main reason causing the disjunctive distribution in section Sciadanthus. F. hupehensis and F. xanthoxyloides are proposed to be relict plants conferred by this process.