Sea-level rise (SLR) from global warming may have severe consequences for biodiversity; however, a baseline, broad-scale assessment of the potential consequences of SLR for island biodiversity is lacking. Here, we quantify area loss for over 12 900 islands and over 3000 terrestrial vertebrates in the Pacific and Southeast Asia under three different SLR scenarios (1 m, 3 m and 6 m). We used very fine-grained elevation information, which offered >100 times greater spatial detail than previous analyses and allowed us to evaluate thousands of hitherto not assessed small islands. Depending on the SLR scenario, we estimate that 15–62% of islands in our study region will be completely inundated and 19–24% will lose 50–99% of their area. Overall, we project that between 1% and 9% of the total island area in our study region may be lost. We find that Pacific species are 2–3 times more vulnerable than those in the Indomalayan or Australasian region and risk losing 4–22% of range area (1–6 m SLR). Species already listed as threatened by IUCN are particularly vulnerable compared with non-threatened species. Under a simple area loss–species loss proportionality assumption, we estimate that 37 island group endemic species in this region risk complete inundation of their current global distribution in the 1 m SLR scenario that is widely anticipated for this century (and 118 species under 3 m SLR). Our analysis provides a first, broad-scale estimate of the potential consequences of SLR for island biodiversity and our findings confirm that islands are extremely vulnerable to sea-level rise even within this century.