Four species of marine calcifying algae, the coccolithophores Calcidiscus leptoporus, Helicosphaera carteri, Syracosphaera pulchra and Umbilicosphaera foliosa were grown in laboratory cultures under temperatures varying between 14 and 23 °C, and one species, C. leptoporus, under varying [CO32−], ranging from 105 to 219 μmol/kg. Calcium isotope compositions of the coccoliths resemble in both absolute fractionation and temperature sensitivity previous calibrations of marine calcifying species e.g. Emiliania huxleyi (coccolithophores) and Orbulina universa (planktonic foraminifera) as well as inorganically precipitated CaCO3, but also reveal small species specific differences. In contrast to inorganically precipitated calcite, but similar to E. huxleyi and O. universa, the carbonate ion concentration of the medium has no statistically significant influence on the Ca isotope fractionation of C. leptoporus coccoliths; however, combined data of E. huxleyi and C. leptoporus indicate that the observed trends might be related to changes of the calcite saturation state of the medium. Since coccoliths constitute a significant portion of the global oceanic CaCO3 export production, the Ca isotope fractionation in these biogenic structures is important for defining the isotopic composition of the Ca sink of the ocean, one of the key parameters for modelling changes to the marine Ca budget over time. For the present ocean our results are in general agreement with the previously postulated and applied mean value of the oceanic Ca sink (Δsed) of about − 1.3‰, but the observed inter- and intra-species differences point to possible changes in Δsed through earth history, due to changing physico-chemical conditions of the ocean and shifts in floral and faunal assemblages.