The Holocene–late Pleistocene distribution of holococcoliths, is quantified by light microscopy from cores from the Western Mediterranean, the Aegean Sea and eight eastern Mediterranean cores recovering sapropel S1. The diversity of fossil holococcoliths is much lower than is seen in the plankton, indicating selective preservation. However the holococcolith phases of Syracosphaera pulchra and Helicosphaera carteri are abundantly preserved allowing a comparison of fossil records of heterococcolith and holococcolith phases of these species. In shallow cores a primary palaeocological signal appears to be preserved, suggesting that under suitable circumstances it is possible to use holococcoliths in palaeoceanography. The common occurrence of holococcoliths in the sapropels from these cores suggests low surface-water productivity, supporting previous inferences that productivity enhancement during sapropel deposition was confined to the deep-chlorophyll maximum. In deeper cores there is dramatic decrease in abundance of S. pulchra holococcoliths within sapropel sediments. From comparison of shallow and deep cores and from Emiliania huxleyi preservation data we conclude that this is a preservation signal. Evidently the calyptroliths produced by S. pulchra have a lower preservation potential than the syracoliths produced by H. carteri, we interpret this as a product of their more open structure.