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Mountain systems throughout the globe are characterized by high levels of species richness and species endemism. Biodiversity, however, is not distributed evenly with altitude, but often declines from mid to high altitudes. Conversely, endemic species may be over-represented at high altitudes. Upward elevational range shifts of mountain species have been reported in response to ongoing changes in climate, yet the reports are dominated by studies on woody species and mountains at high latitudes. We investigated spatial and temporal changes in the mountain biodiversity in the subtropical island of Taiwan, based on historical survey and resurvey data during the period 1906–2006. We found that upper altitudinal limits of mountain plant distributions have risen by ca 3.6 m yr−1 during the last century, in parallel with rising temperatures in the region. Although species, genus, and family richness decline with altitude, ca 55% of species at the highest altitudes are endemic to the island. Given the steep decline in land area with increasing elevation, these high altitude areas are disproportionately important for plant biodiversity when richness and endemism are standardized by available land area. We argue that the distributional shift that we report, in combination with the altitudinal distribution of plant diversity, is likely to pose a major threat to high mountain species of this highly biodiverse island, a threat that is becoming increasingly evident for high mountain plants throughout the globe.