Recent reconstruction of the phylogenetic relationships of hornworts has revealed novel hypotheses of unique common ancestries. The genus Megaceros, for example, was shown to be polyphyletic with New World species nested within Nothoceros. Here we present a sampling of most widely recognized species of both genera to provide a phylogenetic delimitation of Nothoceros and Megaceros based on the genes rbcL and nad5. The unique ancestry shared by Nothoceros and the New World species of Megaceros is confirmed. This clade, except for the New Zealand endemic N. giganteus is restricted to the American continent. The genus Megaceros is redefined to comprise only Asian and Australasian species. The three widely accepted American species of Megaceros, M. aenigmaticus, M. fuegiensis and M. vincentianus are transferred here to Nothoceros. The lack of defining morphological characters for Nothoceros along with its morphological diversity highlights the need for further taxonomic, morphological and ultrastructural studies of the genus.