Biogeographical history and taxonomic delimitation in the Australo-Papuan bird-of-paradise Lophorina-Ptiloris species complex is examined with a combination of DNA and morphological markers. The results suggest that the complex started to diverge in the mid-Pliocene, driven by initial isolation and adaptation to altitudinally different habitats. As in many other New Guinean avian taxa, phylogeographic structure is more varied in montane Lophorina than foothill Ptiloris. With the exception of populations of Lophorina in the eastern New Guinean cordillera, phylogenetic patterns from molecular data and morphological discontinuities are consistently concordant, as are molecular species delimitation tests with previous morphology-based circumscription of taxa in Ptiloris. In Lophorina, however, both molecular data and significant, re-discovered morphological traits identify several taxa as more deeply differentiated than hitherto thought. Accordingly, we use these data in an integrative taxonomic approach to re-delimit taxa in the entire clade, including the recognition of three species in the previously monospecific Lophorina. In Lophorina, the identity of several type specimens is reviewed, one new subspecies is described from the Vogelkop, and the identity of the species name superba Pennant is resolved by neotypification, with correction of its author.