We present a high-resolution study of benthic foraminiferal abundances in 4 cores from the central Aegean and NE Levantine Seas, spanning the interval from 30 ka BP to the present. The benthic foraminiferal faunas indicate that during LGM times, bottom waters were well ventilated, while organic flux to the sea floor was significantly higher than today. From 30 to 10.2 ka BP, faunal density and composition suggest a gradual decrease in organic flux to the sea floor. This trend is interrupted by a short return to higher organic flux levels during the Younger Dryas (12.8–11.5 ka BP). The faunas immediately preceding the early to middle Holocene organic-rich layer (sapropel) S1 are very similar to Late Holocene faunas, indicating oligotrophic conditions. The transition from well ventilated bottom waters to anoxic (Levantine Basin) or strongly dysoxic (Aegean Sea) bottom waters appears to take place within a time-span of only 600 years, from ∼ 10.8 to 10.2 ka BP. Sapropel S1 (10.2–6.4 ka BP) is characterized by extended periods of bottom-water anoxia in the Levantine Basin, and by strongly dysoxic conditions punctuated by episodic re-ventilation events in the Aegean Sea. Re-establishment of fully oxygenated bottom-water conditions after sapropel S1 was extremely rapid. The ensuing Late Holocene faunas are very similar to recent faunas found in the Aegean Sea, suggesting much lower fluxes of organic matter to the sea floor than during glacial times.