Abstract:The relationship of Magnolia wufengensis with several other magnolia species in subgenus Yulania, and the taxon status of M. wufengensis were analyzed with AFLP molecular marker. A collection of 36 accessions representative of 7 magnolia species were selectively amplified and the results showed that 635 out of 874 bands are polymorphic with nine primer combinations; there was a higher genetic similarity between M. wufengensis and M. denudata, M. sprengeri than other magnolia species. The cluster result based on AFLP was generally in harmony with the morphologic taxa in Subgenus Yulania. Not only distinct morphologic differences from other magnolia species but also AFLP molecular markers supported that M. wufengensis should be a new species and M. wufengensis var. wufengensis and M. wufengensis var. multitepala should be the same one species.