The present study aimed to detect and quantify centres of vascular plant species and genus endemism and genus phylogenetic endemism in the New Zealand archipelago and to assess the representation of these in the conservation estate. The presence of 2187 vascular plant species, comprising 213141 georeferenced records, was mapped onto 0.12° grid cells and a genus-level phylogeny was constructed mainly from rbcL sequences used to calculate phylogenetic metrics. Previously identified centres of endemism were confirmed, and new areas of endemism were suggested. Patterns of endemism differ with taxonomic rank. Randomisations showed that the South Island mountains have greater species corrected weighted endemism (CWE) than expected, whereas the randomisations for genus CWE and genus corrected phylogenetic endemism (CPE) showed the northern half of the North Island and northern offshore islands to have greater endemism than expected. Consistent with the randomisations, the highest values of genus CWE and genus CPE predominantly occur in the northern North Island and offshore islands. Centres of species CWE, genus CWE and genus CPE, supported by randomisation analyses, overlap with the New Zealand conservation estate by 40.01, 29.52 and 19.12% respectively. Many areas of high endemism are often poorly protected, highlighting the urgency to consider the areas of endemism identified here in conservation policy, planning and management.