The Initial Eocene Thermal Maximum (IETM) at c. 55 Ma represents a period of rapid global warming that lasted less than 200 ka. The response of vegetation to such an event, and particularly warm-adapted highly diverse vegetation types, is poorly understood. Using pollen floral, clay mineral and stable carbon isotope analyses of sediments from the upper Tuscahoma Formation on the eastern US Gulf Coast (eastern Mississippi and western Alabama), we document paratropical floral changes across the Palaeocene–Eocene boundary from the Wahalak #2 and lower Harrell cores. Data indicate strong changes in the abundance of kaolinite that correlate with changes in relative abundance of native pollen taxa. There is no evidence for a transient, extra-tropical flora on the US Gulf Coast that may characterize the IETM. Immigration and extinction are not associated with this event. Instead, Early Eocene plant immigration occurs in pulses and therefore is not associated directly with climate change during the IETM. The two cores share the same regional species pool but compositional differences are stronger between cores than they are either through changes in environment, increased soil erosion or chemical weathering, or through the introduction of non-native plants. Our data suggest that vegetation change across the Palaeocene–Eocene boundary is not a single event but rather a sequence of cascading events.