We used nuclear and chloroplast DNA markers to examine relationships and test the current morphology-based taxonomy of several species and subspecies of Australian and New Zealand Wahlenbergia. We sampled nuclear ribosomal ITS regions and the chloroplast regions trnL–F and trnK–psbA from 105 individuals, representing 29 of the 46 species and subspecies currently recognised in New Zealand and Australia. Our phylogeny was incompletely resolved because of low levels of genetic variation in all three markers and some conflict between ITS and chloroplast markers. The New Zealand rhizomatous species appear to have radiated in New Zealand after a single long-distance dispersal event from Australia, but it is unclear to which species in Australia they are most closely related. The New Zealand radicate species do not form a clade; instead they are shown to be very closely related to many Australian radicate species. The four species in the New Zealand lowland radicate W. gracilis complex may all belong to the same morphologically variable species. In contrast, the other New Zealand radicate species, W. vernicosa, is probably a separately evolving lineage, and is not conspecific with the W. gracilis complex, nor the Australian W. littoricola, as previously hypothesised. Two of the New Zealand rhizomatous species, W. albomarginata and W. pygmaea, may be conspecific. By contrast, the morphologically distinctive New Zealand rhizomatous W. cartilaginea, W. matthewsii and W. congesta subsp. haastii each formed monophyletic groups. Samples of two recently described Australian species (W. rupicola and W. telfordii) formed monophyletic groups consistent with their recognition.