More than one thousand specimens of a morphological complex including Galeacysta etrusca Corradini & Biffi 1988 from 11 Upper Miocene and Lower Pliocene localities of the Paratethyan and Mediterranean realms have been studied using a biometric approach in part relating to the degree of separation between endocyst and ectocyst. Four stable biometric groups have been distinguished statistically, the occurrence or prevalence of which appears closely linked to environmental conditions irrespective of the realm. Group ‘a' is related to brackish conditions, group ‘b' to marine conditions, group ‘c' to freshwater, and group ‘d' to high nutrient levels. Based on an accurate chronology provided by calcareous nannoplankton bioevents and recognition of the Messinian Erosional Surface, this study reveals: 1. the high sensitivity of the Galeacysta etrusca complex for reconstructing paleoenvironments and discriminating phases of connection and isolation of basins; 2. the detailed history of this species complex which originated in the Pannonian Basin at ca. 8 Ma before invading the Dacic Basin during the interval 6–5.60 Ma, then migrating into the Mediterranean during high sea-level connections (the ‘Lago Mare' events just before and after the peak of the Messinian Salinity Crisis, i.e. at 5.60 Ma and during the interval ca. 5.46–5.278 Ma, respectively), and finally into the Black Sea at ca. 5.13 Ma; 3. an improved paleogeography for the Mediterranean and Paratethyan realms with focus on the location of corridors and the timing of when they were active. Based on field observations and dinoflagellate cyst data, we propose that the reflooding of the Mediterranean Basin by Atlantic waters occurred at ca. 5.46 Ma, about 130 kyr before the Zanclean GSSP (5.332 Ma).