During the late Paleocene thermal maximum (ca. 55.50 Ma) mid-bathyal ostracodes at Maud Rise in the Southern Ocean (Ocean Drilling Program Site 689) underwent a sudden, dramatic turnover synchronous with a global extinction in deep-sea benthic foraminifers and with large-scale, short-lived negative excursions in the stable isotope record of foraminiferal calcite. A previously stable and long-lived ostracode assemblage, dominated by heavily calcified, chiefly epifaunal taxa, was replaced within ∼ 10 k.y. by a taxonomically novel association of small, thin-walled opportunistic and generalist forms that persisted for ∼ 25–40 k.y. Thereafter, ostracode faunas recovered and common bathyal forms returned, although species were smaller and/or less-heavily calcified than before the turnover. The complex fabric of change in ostracode shell morphology and assemblage composition and structure reflects both long-term and sudden perturbations in seawater chemistry at this site. Ostracode data are in agreement with the hypothesis that the latest Paleocene extinctions in the deep sea were caused by a change in the dominant source area of intermediate water mass from high altitudes to the subtropics. These data also suggest that warm saline waters persisted at Maud Rise for the next 100 k.y.