Islands are some of the most biodiverse places on earth, but they are also hotspots of biodiversity loss. The coastline of Florida, U.S.A., is surrounded by thousands of islands, many of which are home to species that occur nowhere else. A rapidly emerging threat to these low-lying islands is inundation as sea levels rise. The capacity of island-dwelling species to adapt to climate change and sea level rise may be limited because many species do not have the ability to shift their distribution off the island to track favorable conditions. We assessed the vulnerability of Florida’s islands to inundation from sea level rise and estimated the terrestrial biodiversity on Florida’s islands that could be lost. Our models predicted that by 2100, over 80% and up to 90% of Florida’s islands could be completely inundated from sea level rise, depending on the sea level rise projection (1.2 m or 2.2 m). Of the 85 mammalian, reptilian, and amphibian species on our subset list of Florida’s Species of Greatest Conservation Need, over half occur on Florida’s islands for at least part of their range, highlighting the importance of these islands for housing Florida’s rich biodiversity. Notably, at least 12 mammal species and 7 reptile species have their entire distribution on Florida’s islands, and this count is likely an underestimate. Projections of future sea level rise mean that these island-endemic species face the threat of extinction in the wild if their island habitat is submerged.