A remarkable oxygen and carbon isotope excursion occurred in Antarctic waters near the end of the Palaeocene (~57.33 Myr ago), indicating rapid global warming and oceanographic changes that caused one of the largest deep-sea benthic extinctions of the past 90 million years. In contrast, the oceanic plankton were largely unaffected, implying a decoupling of the deep and shallow ecosystems. The data suggest that for a few thousand years, ocean circulation underwent fundamental changes producing a transient state that, although brief, had long-term effects on environmental and biotic evolution.