The expected upward shift of trees due to climate warming is supposed to be a major threat to range-restricted high-altitude species by shrinking the area of their suitable habitats. Our projections show that areas of endemism of five taxonomic groups (vascular plants, snails, spiders, butterflies, and beetles) in the Austrian Alps will, on average, experience a 77% habitat loss even under the weakest climate change scenario (+1.8 °C by 2100). The amount of habitat loss is positively related with the pooled endemic species richness (species from all five taxonomic groups) and with the richness of endemic vascular plants, snails, and beetles. Owing to limited postglacial migration, hotspots of high-altitude endemics are situated in rather low peripheral mountain chains of the Alps, which have not been glaciated during the Pleistocene. There, tree line expansion disproportionally reduces habitats of high-altitude species. Such legacies of climate history, which may aggravate extinction risks under future climate change have to be expected for many temperate mountain ranges.