In previous attempts to correlate fluctuations of climate with the carbonate content of deep-sea sediments, using the ratio 18O/16O as an indicator of palaeotemperature, conflicting patterns have emerged between Pacific and Atlantic deep-sea cores. Although there is controversy about the relative importance of the primary productivity of calcareous microorganisms1–3 and their dissolution at depth4–10, in Pacific Pleistocene cores high-carbonate sediments correlate with glacial episodes and low-carbonate sediments with interglacials1–4,7–10. In Atlantic Pleistocene cores, on the other hand, the correlation seems to be re versed4,5,7,10–12. We report here that a late Miocene (6.14–6.53 Myr) deep-sea sediment core from the eastern equatorial Pacific (DSDP Site 158) shows a negative correlation between carbonate content and benthic oxygen isotopes which is similar to that found in Quaternary records of the Atlantic rather than the Pacific. The explanation may be that Atlantic and Pacific waters differed in HCO3− concentration at depth as they do today, and that in the late Miocene, Atlantic water flowed over the submarine sill at the Isthmus of Panama and at least periodically, reached the location of Site 158.