The ratite moa (Aves; Dinornithiformes) were massive graviportal browsers weighing up to 250kg (ref. 1) that dominated the New Zealand biota until their extinction approximately 500yr ago. Despite an extensive Quaternary fossil record, moa taxonomy remains problematic and currently 11 species are recognized. Three Dinornis species were found throughout New Zealand and differed markedly in size (1-2m height at back) and mass (from ~34 to 242kg). Surprisingly, ancient mitochondrial DNA sequences show that the three species were genetically indistinguishable within each island, but formed separate North and South Island clades. Here we show, using the first sex-linked nuclear sequences from an extinct species, that on each island the three morphological forms actually represent just one species, whose size varied markedly according to sex and habitat. The largest females in this example of extreme reversed sexual size dimorphism were about 280% the weight and 150% the height of the largest males, which is unprecedented among birds and terrestrial mammals. The combination of molecular and palaeontological data highlights the difficulties of analysing extinct groups, even those with detailed fossil records.