The Paleocene - Eocene Thermal Maximum (PETM; 56 Ma) was a phase of rapid global warming associated with massive carbon input into the ocean-atmosphere system from a 13C-depleted reservoir. Many mid- and high-latitude sections have been studied and document changes in salinity, hydrology and sedimentation, deoxygenation, biotic overturning and migrations, but detailed records from tropical regions are lacking. Here, we study the PETM at Ocean Drilling Program (ODP) Site 959 in the equatorial Atlantic using a range of organic and inorganic proxies and couple these with dinoflagellate cyst (dinocyst) assemblage analysis. The PETM at Site 959 was previously found to be marked by a ~3.8 per mil negative carbon isotope excursion (CIE), and a ~4 ºC surface ocean warming from the uppermost Paleocene to peak PETM, of which ~1 ºC occurs before the onset of the CIE. We record upper Paleocene dinocyst assemblages that are similar to PETM assemblages as found in extra-tropical regions, confirming poleward migrations of ecosystems during the PETM. The early stages of the PETM are marked by a typical acme of the tropical genus Apectodinium, which reaches abundances of up to 95 %. Subsequently, dinocyst abundances diminish greatly, as do carbonate and pyritized silicate microfossils. The combined paleoenvironmental information from Site 959 and a close by shelf site in Nigeria implies the general absence of eukaryotic surface-dwelling microplankton during peak PETM warmth is most likely caused by heat stress. Crucially, abundant organic benthic foraminiferal linings imply sustained export production, likely driven by prokaryotes. In sharp contrast, the recovery of the CIE yields rapid (<<10 kyr) fluctuations in the abundance of several dinocyst groups, suggesting extreme ecosystem and environmental variability.