The Ypresian-Lutetian (Y-L; early-middle Eocene) transition was a pivotal time in global climate development, because at that time a process of global cooling initiated, ending the Early Eocene Climate Optimum and culminating in the early Oligocene Glacial Maximum, at which time polar sheets on Antarctica first reached sea-level. We document benthic foraminiferal assemblages and stable isotope data on samples from cores taken at upper and lower abyssal depths on Walvis Ridge (SE Atlantic, IODP Leg 208) across the Y-L transition. The isotopic record and the occurrence of specimens intermediate in morphology between N. truempyi (extinct in the latest Eocene) and its extant descendant N. umbonifera, indicator of corrosive bottom waters (e.g., Antarctic Bottom Water), as well as various Epistominella species, suggest that palaeoceanographic and climatic changes leading to the initiation of Antarctic glaciation may have started during the Y-L transition. Typically early Eocene species persisted into the Lutetian at the deeper site, bathed by bottom waters, whereas they had their last appearances at the Y/L boundary at the shallower site, bathed by intermediate waters. The overall cooling at southern high latitudes thus may have led to initiation of circulation changes at intermediate depths before bottom waters were affected.