Phylogenetic analyses of ITS and 5′ trnK/matK spacer sequences were undertaken for 39 species representing the range of morphological variation in the genus Brachyglottis and putative outgroups. Independent analyses of the sequence data were largely congruent, and when combined provided stronger support for relationships. The results suggest that Brachyglottis as currently circumscribed is paraphyletic. However, a more inclusive monophyletic group was supported that consists of the genera Bedfordia, Brachyglottis, Dolichoglottis, Haastia, and Traversia. Short branch lengths suggest that there has been a spectacular adaptive radiation of the Brachyglottis alliance in recent times. The species are morphologically diverse and occupy a wide range of ecological niches in New Zealand, yet exhibit very little sequence variation.