Aim To detect centres of vascular plant endemism at a continental scale by analysis of specimen-based distributional data and to relate any pattern to environmental factors and history.Location Australia.Methods Presence of 8468 seed plant species-level taxa throughout continental Australia and Tasmania was mapped on a 1° grid to visualize the pattern of species richness. This sample comprises half the known flora. Three indices of endemism were calculated but we preferred one that is unrelated to species richness, so that these two concepts could be distinguished in practice. Centres of endemism were detected by simple mapping and by spatial autocorrelation analysis (SAC). Linear regression was used to examine the relationship of the patterns of species richness and endemism to latitude, topography and climate.Results Both species richness and endemism vary greatly across the continent but in most cases the same centres were high in both richness and endemism. Twelve distinct centres were identified. The major centres of both diversity and endemism are south-west western Australia, the Border Ranges between New South Wales and Queensland, the Wet Tropics near Cairns, Tasmania and the Iron-McIlwraith Range of eastern Cape York Peninsula. The last centre appears to be more significant than recognized by past authors. Whether this is a true Australian centre of endemism, or is largely an outlier of the flora of Papua New Guinea, is explored. Another centre, in the Adelaide–Kangaroo Island region, has been overlooked altogether by previous authors. Regression analysis did not find a simple climatic explanation of the observed patterns. There was a suggestion that topographic variation within the 1° cells may be positively correlated with endemism, which is consistent with mountainous regions functioning as refugia. One clear result is that all the major centres of endemism are near-coastal. A likely explanation is that Pleistocene expansions of the central desert have been a powerful limitation on the viability of refugia for narrowly endemic species. All the centres of endemism lie outside the estimated limits of the expanded arid zone at the last glacial maximum (18,000 yr BP). In particular, the `Central Australian Mountain Ranges centre of plant diversity and endemism' of Boden & Given (1995) is detected as a strong centre of species richness, but not at all as a centre of endemism. This is despite good sampling of this region.Main conclusions Endemism can be distinguished from species richness by using an appropriate index and mapping of such indices can detect centres of endemism. This study demonstrates the value of specimen based distributional data, such as is held in state herbaria and museums.