The extent to which the Messinian salinity crisis modified the initially Tethyan, eastern Mediterranean phytoplankton community has been investigated by monitoring the fate of calcareous dinoflagellate cyst assemblages prior to, during and after the salinity crisis in the Pissouri section (Cyprus). A rich, but low diversity open oceanic assemblage, dominated by Calciodinellum albatrosianum, is found in the upper Tortonian and lower Messinian. The upper Messinian (pre-evaporitic) sediments yield only few cysts but the assemblage is much more diverse and reflects unstable more neritic conditions (Bicarinellum tricarinelloides), fluvial influence (Leonella granifera) and varying, temporally increased salinities (Pernambugia tuberosa), probably related to the increasingly restricted environment. The basal Pliocene sediments reflect the return to normal marine conditions; the dinoflagellate assemblage is rich in cysts and again has a low diversity. However, in contrast to the C. albatrosianum-dominated upper Tortonian and pre-evaporitic Messinian sediments, L. granifera clearly dominates the basal Pliocene association just after the replenishment of the Mediterranean basin. Apart from this shift in dominance, the onset of the Pliocene is furthermore marked by the first appearance of Calciodinellum elongatum, which must have immigrated from the Atlantic Ocean. Lebessphaera urania, a postulated remnant of the Tethyan Ocean survived the salinity crisis, possibly in as yet unidentified marine refuges in the Mediterranean itself. Although the environmental changes caused by the Messinian salinity crisis did not lead to an extinction of calcareous dinoflagellate species of the Pissouri Basin, it resulted in a significant change in the assemblages and contributed to a more modern character of the Pliocene dinoflagellate association in the eastern Mediterranean.