Lepidium sisymbrioides, a New Zealand endemic, is the sole dioecious species in Brassicaceae and, therefore, the closest dioecious relative of the model plant Arabidopsis thaliana. The attractiveness of developing this system for future studies on the genetics of sex determination prompted us to investigate historical and developmental factors surrounding the evolution of its unisexual flowers. Our goal was to determine the pattern of polyploidization of L. sisymbrioides and the timing and process of flower reproductive organ abortion. To that end, we used a combination of phylogenetic and histological approaches to place this species within the complex history of polyploidization events in Lepidium and to comparatively characterize its floral ontogeny to that of its closest hermaphroditic relatives and to A. thaliana.