Global biodiversity hotspots (GBHs) are increasingly vulnerable to human stressors such as anthropogenic climate change, which will alter the ecology of these habitats, even where protected. The longleaf pine (Pinus palustris) ecosystem (LPE) of the North American Coastal Plain is a GBH where disturbances are integral for ecosystem maintenance. However, stronger storms due to climate change may be outside their historical norm. In this study, we estimate the extent of Florida LPE that was directly affected by Hurricane Michael in 2018, an unprecedented Category 5 storm. We then leveraged a unique data set in a Before-After study of four sites within this region. We used variable-area transects and generalized linear mixed-effects models to estimate tree densities and logistic regression to estimate mortality by size class. We found at least 28% of the global total remaining extent of LPE was affected in Florida alone. Mortality was highest in medium sized trees (30-45 cm dbh) and ranged from 4.6-15.4% at sites further from the storm center, but increased to 87.8% near the storm center. As the frequency and intensity of extreme events increases, management plans to mitigate climate change need to account for large-scale stochastic mortality events to preserve critical habitats.