Recent molecular studies have redefined families and genera within the anthocerotes, but species boundaries are only now being revised. Monophyly of Australian and New Zealand taxa within the genus Megaceros Campb., which share the same spore and similar gametophyte morphology, was assessed. On the basis of sequence data, mainland Australian lineages are not monophyletic but are interspersed with New Zealand lineages. There are three species present in Australia, including the common and widespread M. gracilis (Reichardt) Steph., the widespread tropical M. flagellaris (Mitt.) Steph., recognised by its tesselated spores, and a new species, M. austronesophilus, found only in Tasmania and Macquarie Island. None of the currently recognised New Zealand taxa is conspecific with any of the Australian taxa. However, New Zealand lineages were found to be genetically and morphologically more diverse than is currently recognised.