Modern global change threatens alpine ecosystems by forcing species to migrate to higher elevations and potentially eliminating alpine habitat altogether. Here we show that an analogous restriction of suitable habitat operates on submarine mountains. During the Paleocene–Eocene Thermal Maximum (PETM, ca. 55.96 Ma), ostracodes underwent local extinction on the crest of Allison Guyot in the central Pacific Ocean, which lost 64% of its ostracode species richness (14 species reduced to three species) and as much as 94% of ostracode abundance for ∼1.1 m.y., before recolonization rebuilt biodiversity and abundance over the next 200 k.y. Biotic changes may reflect an increase in current speeds, acidification, and a decrease in food supply owing to a temperature-driven increase in metabolic rates. Notably, continental margin ostracodes also underwent extinction during the PETM (25%–38% loss) but, unlike Allison Guyot faunas, could quickly repopulate the continental slope. The absence of refugia for isolated seamounts prolonged the reduction in biodiversity initiated by the PETM, a pattern that may be expected for modern seamount faunas in an era of future global change.