The distributions of the 567 plant species considered to be endemic to the Northern Territory, Australia, were collated from a distributional database comprising about 600 000 records. Endemic species comprise a non-random taxonomic subset of all plants known from the Northern Territory. Because of substantial geographic disparity in collecting effort, we analysed geographic patterning of these endemic species by using both (1) actual records only and (2) interpolated ranges (minimum convex polygons). The geographic distribution of the number of Northern Territory endemic plant species was well predicted by a measure of topographic complexity and climate (particularly rainfall). The observed distributional patterning of endemic species was also influenced by survey effort, but this latter influence was substantially reduced by the use of minimum convex polygons. Both analyses revealed that there was a clear aggregation of endemic species in the 32 000 km² of the sandstone plateau of western Arnhem Land. This ‘hotspot’ has been previously recognised in coarser-scale assessments of national and international centres of plant biodiversity. Our analysis concluded that 172 species are restricted to this plateau, and that the plateau comprised at least 90% of the distribution of a further 25 species. More broadly, 438 plant species are endemic to the northern part of the Northern Territory (the 316 000 km² north of 16°S), a level of endemism that may match that of Cape York Peninsula and surpasses that of the Kimberley. The core area for Northern Territory endemic plants, the plateau of western Arnhem Land, is currently threatened, particularly by unfavourable fire regimes.