End-Permian (ca. 252 Ma) carbon isotope, paleobiological, and sedimentary data suggest that changes in ocean carbonate chemistry were directly linked to the mass extinction of marine organisms. Calcium isotopes provide a geochemical means to constrain the nature of these changes. The δ44/40Ca of carbonate rocks from southern China exhibits a negative excursion across the end-Permian extinction horizon, consistent with either a negative shift in the δ44/40Ca of seawater or a change in the calcite/aragonite ratio of carbonate sediments at the time of deposition. To test between these possibilities, we measured the δ44/40Ca of hydroxyapatite conodont microfossils from the global stratotype section and point (GSSP) for the Permian-Triassic boundary at Meishan, China. The conodont δ44/40Ca record shows a negative excursion similar in stratigraphic position and magnitude to that previously observed in carbonate rocks. Parallel negative excursions in the δ44/40Ca of carbonate rocks and conodont microfossils cannot be accounted for by a change in carbonate mineralogy, but are consistent with a negative shift in the δ44/40Ca of seawater. Such a shift is best accounted for by an episode of ocean acidification, pointing toward strong similarities between the greatest catastrophe in the history of animal life and anticipated global change during the twenty-first century.