Abstract Woonyoungia septentrionalis (Dandy) Law is a dioecious species with unisexual flowers in Magnoliaceae. The floral morphology and structure of the species are conspicuously different from other species and are important to the study of floral phylogeny in this family. The floral anatomy and ontogeny were investigated to evaluate the systematic position of W. septentrionalis, using scanning electron microscopy and light microscopy. All of the floral organs are initiated acropetally and spirally. The carpels are of conduplicated type without the differentiation of stigma and style. The degenerated stamens in the female flowers have the same structures as the normal stamens at the earlier developmental stages, but they do not undergo successive development and eventually degenerate. The male floral apex was observed to have the remnants of carpels in a few investigated samples. As the bisexual flower features could be traced both in the male and female flowers in W. septentrionalis, it suggests that the flower sex in Magnoliaceae tends toward unisexual. As well as the unisexual flowers, the reduced tepals and carpels and concrescence of carpels conform to the specialized tendency in Magnoliaceae, which confirms the derived position of W. septentrionalis in this family. As the initiation pattern of floral parts of W. septentrionalis is very similar to other species in this family, it needs further investigation and especially comparison with species in Kmeria to evaluate the separation of Woonyoungia.