The Palaeocene–Eocene Thermal Maximum (PETM) at c. 55.8 Ma marks a transient (c. 100 ka duration) interval of rapid greenhouse warming that had profound effects on marine and terrestrial biota. Plant communities responded rapidly with major compositional turnover. The long-term effects on tropical vegetation communities that stem from the brief period of global warming are unclear. We present pollen data from the paratropical US Gulf Coast (eastern Mississippi, western Alabama and Georgia), which had background Palaeogene mean annual temperatures of 26–27 °C. Sporomorph data (pollen and spores) demonstrate that taxonomic diversity increases over c. 1 Ma in the Late Palaeocene but this trend is replaced, with the first occurrences of taxa that mark the Early Eocene, by a pronounced extinction into the Early Eocene (c. 20% of the palynoflora). Taxonomic diversity also decreases by up to 38% in the Early Eocene. The timing of the extinction is not clearly resolved but may be restricted to the earliest part of the Early Eocene. Two richness estimators (Chao 2 and Jackknife 2) both demonstrate that Late Palaeocene samples contain significantly more taxa than those in the Early Eocene. Extinction on the US Gulf Coast proves that ancient tropical ecosystems were highly susceptible to changes in diversity mediated directly or indirectly by environmental change even during equable greenhouse climates in the early Palaeogene.