The Amentotaxus argotaenia (Taxaceae) species complex is comprised of four relict and endangered gymnosperms. Amentotaxus argotaenia and A. yunnanensis are scattered throughout South and Central China, and A. formosana, and A. poilanei are restricted to Taiwan and Vietnam. In the present study, we examined genetic divergence and biogeographical patterns in the species complex based on chloroplast DNA atpI-atpH and rpS16-trnK intergenic spacers, the mitochondrial DNA nad1 intron, and microsatellite markers. Genealogical analyses revealed systematic inconsistencies between organellar DNA markers, with paraphyletic species inferred based on cpDNA, versus a monophyletic A. formosana, and clustering of A. poilanei within A. yunnanensis at mtDNA. AMOVA revealed that most organellar DNA variants resided among species and populations, a pattern also supported by clustering with STRUCTURE analyses on microsatellites. Higher levels of genetic diversity in the Yongxin population of A. argotaenia reflected features of a refugium. Most speciation events were rather recent, with divergence no earlier than 2.50 MYA, although many ancient lineages derived 4.12-13.84 MYA were maintained within species. Significant genetic structuring within A. argotaenia was detected among three geographical regions-a phylogeographical pattern likely attributable to past fragmentations. In contrast to paraphyletic A. argotaenia based on the maintenance of ancestral polymorphisms, interspecific hybridization likely contributed to polyphyly in A. yunnanensis. Furthermore, despite the low likelihood of recurrent gene flow due to geographical isolation, IM analyses revealed continued interspecific gene flow after species divergence, reflecting a parapatric speciation model.