The placement of Nartheciaceae within Dioscoreales is an unexpected result of molecular phylogenetics. Nartheciaceae generally differs from the rest of Dioscoreales in having less specialized flowers. Studies of this family are important to elucidate the evolutionary history of the order. Using scanning electron microscopy and light microscopy, we describe the details of the flower structure, initiation, and development in Metanarthecium, which is unique amongst Nartheciaceae in possessing both an almost superior ovary and septal nectaries. This is the first member of Dioscoreales for which all stages of organogenesis have been studied. Within Nartheciaceae, the presence/absence of septal nectaries and the position of the ovary are labile. The presence of post-genital fusion in the gynoecium correlates with the presence of septal nectaries. Septal nectary morphology is complicated in Metanarthecium, which raises the question of whether its floral structure (including superior ovary) is plesiomorphic within Dioscoreales. The septal nectaries of Metanarthecium show homoplastic similarity with those of Allium (Asparagales). The presence/absence of a compitum is probably variable at the infraspecific level in Metanarthecium as a result of alternative possibilities of post-genital fusion between ventral carpel margins. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 158, 1–18.