The small genus Chrysanthemoides comprises two species within which a number of infraspecific taxa have been recognized, some of which are invasive aliens in Australia and New Zealand. Here we investigate the relationships of the species and infraspecific taxa using both chloroplast and nuclear non-coding DNA sequence data. Results of the analyses of the plastid and nuclear data sets are incongruent, and neither Chrysanthemoides nor Osteospermum is resolved as monophyletic, although there is some support for the recognition of infraspecific taxa. Analyses of the separate and combined data sets resolve two clades within Chrysanthemoides (which include some species of Osteospermum), and these appear to have a geographic basis, one being restricted to the mainly winter rainfall region, the other the eastern bi-seasonal rainfall area. Our results suggest that there is evidence of past or ongoing hybridization within and possibly between these two lineages.