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Biodiversity hotspots are conservation priority areas that meet two criteria: they must have lost >= 70% of their primary vegetation, and they must contain >= 1500 endemic vascular plant species. Given the limited time and resources available for conservation and predicted future land-use change, it is necessary for conservation efforts in biodiversity hotspots to become more effective. In this study, we identified regions that have lost 70% of their primary vegetation and in which the past endemic vascular plant species richness was estimated to be higher than the biodiversity hotspot threshold of 1500 species (i.e., regions that were possible biodiversity hotspots). Next, we compared historical land-use change data from 1500 to 2010 between the identified regions and biodiversity hotspots. We found that the rate of land-use change in the biodiversity hotspots was significantly lower than that in the identified regions, suggesting that rapid land-use change poses an increased threat to endemic plants and is associated with the loss of endemic plant diversity. Biodiversity hotspots thus likely maintain many species that are vulnerable to rapid land-use change. Fortunately, some identified regions have not experienced rapid land-use change and thus have the potential to be newly recognized as biodiversity hotspots: the Altai-Sayan Montane Forests, the Amur-Heilong River Basin, and the Southeast China Subtropical Forests. Our findings reinforce the importance of prioritizing biodiversity hotspots for conservation and emphasize the need to develop efficient conservation strategies specialized to mitigate the effects of rapid land-use change on biodiversity.