Within Australia there are 19 endemic species of Anseriformes. Six of these belong to monotypic genera, some of which remain controversial with respect to phylogenetic relationships. Sequence variation in a 307-base pair fragment of the cytochrome-b gene was compared from 23 species of waterfowl (the Cairina sequence was obtained from the literature) to elucidate further the relationships of these monotypic Australian genera. Anseranas and Dendrocygna were identified as the earliest diverged genera among the taxa examined. The remaining genera fell into two groups: (1) Tadorna, Alopochen, Chenonetta, Anas, Aythya, Cairina and Air and (2) Cygnus, Branta, Cereopsis, Biziura, Oxyura, Malacorhynchus, Stictonetta and Nettapus. The controversial nature of the last group is discussed.