Categorical analysis of neo- and palaeo-endemism (CANAPE), phylogenetic diversity (PD) and phylogenetic weighted endemism (PWE) were used to explore patterns of diversity, endemism and biogeography in the indigenous vascular flora of the New Zealand archipelago. Distributional data comprising 213 142 records for 436 genera and 2187 species and a phylogeny based mainly on rbcL sequences were used to calculate neo- and palaeo-endemism biodiversity metrics for 0.12° grid cells. Genus- and species-level analyses of PD revealed few significantly high-value cells mostly scattered in the northern North Island, and, for PWE, significantly high-value cells were concentrated in the northern North Island and northern offshore islands. CANAPE analyses suggested that palaeo-endemism is concentrated in northern North Island and the northern offshore islands, whereas neo-endemism is concentrated in South Island and the southern offshore islands. The areas of endemism highlighted by our analyses are compared with earlier biogeographic studies of endemism in the New Zealand flora. Some revision of previously suggested biogeographic boundaries is proposed, with the boundaries of the central South Island alpine gap being further north than previous studies have inferred, and the possibility that Pliocene marine transgression contributed to shaping the central North Island palaeo-endemism boundary is discussed.