Anthropogenic climate change is predicted to cause widespread biodiversity loss due to shifts in species’ distributions, but these predictions rarely incorporate ecological associations such as zonation. Here, we predict the decline of a diverse assemblage of mid-latitude salt marsh plants, based on an ecosystem warming experiment. In New England salt marshes, a guild of halophytic forbs occupies stressful, waterlogged pannes. At three sites, experimental warming of < 4 °C led to diversity declines in pannes and rapid takeover by a competitive dominant, Spartina patens. In Rhode Island, near their southern range limit, pannes were more sensitive to warming than farther north, and panne area also declined in control plots over the three-season experiment. These results suggest that warming will rapidly reduce plant diversity in New England salt marshes by eliminating a high diversity zone. Biodiversity in zoned ecosystems may be more affected by climate-driven shifts in zonation than by individual species’ distribution shifts.