The shells of the planktonic foraminifer Neogloboquadrina pachyderma have become a classical tool for reconstructing glacial–interglacial climate conditions in the North Atlantic Ocean1–3. Palaeoceanographers utilize its left- and right-coiling variants, which exhibit a distinctive reciprocal temperature and water mass related shift in faunal abundance both at present and in late Quaternary sediments1,2,4,5. Recently discovered cryptic genetic diversity in planktonic foraminifers6–8 now poses signifi- cant questions for these studies. Here we report genetic evidence demonstrating that the apparent ‘single species’ shell-based records of right-coiling N. pachyderma used in palaeoceanographic reconstructions contain an alternation in species as environmental factors change. This is reflected in a speciesdependent incremental shift in right-coiling N. pachyderma shell calcite d 18O between the Last Glacial Maximum and full Holocene conditions. Guided by the percentage dextral coiling ratio, our findings enhance the use of d 18O records of rightcoiling N. pachyderma for future study. They also highlight the need to genetically investigate other important morphospecies to refine their accuracy and reliability as palaeoceanographic proxies.