The latest Paleocene benthic foraminiferal extinction event has been studied in two marlstone successions in the Tethys: at Wadi Nukhl (Egypt) and Torangly (Turkmenistan). Both sections yield a sapropelic layer at the level of the extinction event. At Nukhl, this layer underlies a thin calcareous bed that has also been found in other Middle East upper Paleocene sections. With the onset of anoxia at the Tethyan sea floor, the aerobic and oligotrophic Gavelinella beccariiformis deep-sea community collapsed. Eutrophic-to-mesotrophic and low-oxygen conditions, most likely resulting from enhanced organic carbon fluxes to the sea floor, triggered an ∼100–200 k.y. repopulation sequence, marked by downslope migration of several neritic communities that were dominated by opportunistic and tolerant taxa. The initial ecosystem restoration was completed when an aerobic and oligotrophic Nuttallides truempyi deep-sea community became established. We suggest that this repopulation mode could be typical for the central Tethys.