Despite the increasing interest in the South Atlantic Ocean as a key area of the heat exchange between the southern and the northern hemisphere, information about its palaeoceanographic conditions during transitions from glacial to interglacial stages, the so-called Terminations, are not well understood. Herein we attempt to increase this information by studying the calcareous dinoflagellate cysts and the shells of Thoracosphaera heimii (calcareous cysts) of five Late Quaternary South Atlantic Ocean cores. Extremely high accumulation rates of calcareous cysts at the Terminations might be due to a combined effect of increased cyst production and better preservation as result of calm, oligotrophic conditions in the upper water layers. Low relative abundance of Sphaerodinella albatrosiana compared with Sphaerodinella tuberosa in the Cape Basin may be the result of the relatively colder environmental conditions in this region compared with the equatorial Atlantic Ocean with high relative abundance of S. albatrosiana. Furthermore, the predominance of S. tuberosa during glacials and interglacials at the observed site of the western Atlantic Ocean reflects decreased salinity in the upper water layer.