The Latest Danian Event (LDE) is a proposed early Palaeogene transient warming event similar to the Paleocene–Eocene Thermal Maximum, albeit of smaller magnitude. The LDE can be correlated with a carbon isotope excursion (‘CIE-DS1’) at Zumaia, Spain, and the ‘top Chron C27n event’ defined recently from ocean drilling sites in the Atlantic and Pacific, supporting a global extent. Yet, records of environmental change during the LDE (e.g. warming and sea-level fluctuations) are still rare. In this study, we focus on the micropalaeontology (calcareous nannofossils and benthic foraminifera), mineralogy and trace element geochemistry of the LDE in the Qreiya 3 section from the southern Tethyan margin in Egypt. In this section, the LDE is characterized by the occurrence of anomalous beds intercalated within upper Danian shales and marls. The event beds of the LDE are situated above an unconformity on top of a shallowing-upwards sequence deposited in a well-oxygenated outer neritic to upper bathyal marine palaeoenvironment. The lower LDE bed is barren of benthic foraminifera, but contains pyrite and fish remains, and is interpreted as an anoxic level formed during rapid relative sea-level rise. Incursion of a Neoeponides duwi (Nakkady, 1950) benthic assemblage in LDE bed II is interpreted as repopulation of the seafloor after anoxia. The sea-level cycle associated with the LDE is estimated at about 50?m maximum in the Qreiya 3 section. The environmental changes at Qreiya 3 are of supra-regional extent, since a similar sequence of events has been observed at other southern Tethyan locations.