To investigate the potential use of the stable isotope composition of the vegetative cysts of the photosynthetic dinoflagellate Thoracosphaera heimii for quantitative palaeotemperature reconstructions a method has been developed to purify T. heimii cysts from sediment samples. Stable oxygen and carbon isotopes have been measured on T. heimii cysts from 21 surface sediment samples from the equatorial Atlantic and South Atlantic Oceans. Calculated temperatures based on the palaeotemperature equation for inorganic calcite precipitation generally reflect mean annual temperatures of the upper water column, notably of thermocline depths. Although the present results suggest that the isotopic composition of T. heimii shells might be formed in equilibrium with the seawater in which the shells are being formed, future investigations are required to determine possible effects of metabolic and kinetic processes on the fractionation process. This pilot study therefore forms the basis for future investigations on the development of this tool and the determination of a species-specific palaeotemperature equation. The wide geographic and stratigraphic distribution of T. heimii cysts in sediments, the stable position of T. heimii within the water column and the high resistance of its cysts against calcite dissolution underline its potential for a wide usability in palaeotemperature reconstructions