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This integrated study (field observations, micropalaeontology, magnetostratigraphy, geochemistry, borehole data and seismic profiles) of the Messinian–Zanclean deposits on Zakynthos Island (Ionian Sea) focuses on the sedimentary succession recording the pre-evaporitic phase of the Messinian salinity crisis (MSC) through the re-establishment of the marine conditions in a transitional area between the eastern and the western Mediterranean. Two intervals are distinguished through the palaeoenvironmental reconstruction of the pre-evaporitic Messinian in Kalamaki: (a) 6.45–6.122 Ma and (b) 6.122–5.97 Ma. Both the planktonic foraminifer and the fish assemblages indicate a cooling phase punctuated by hypersalinity episodes at around 6.05 Ma. Two evaporite units are recognized and associated with the tectonic evolution of the Kalamaki–Argassi area. The Primary Lower Gypsum (PLG) unit was deposited during the first MSC stage (5.971–5.60 Ma) in late-Messinian marginal basins within the pre-Apulian foreland basin and in the wedge-top (<300 m) developed over the Ionian zone. During the second MSC stage (5.60–5.55 Ma), the PLG evaporites were deeply eroded in the forebulge–backbulge and the wedge-top areas, and supplied the foreland basin's depocentre with gypsum turbidites assigned to the Resedimented Lower Gypsum (RLG) unit. In this study, we propose a simple model for the Neogene–Pliocene continental foreland-directed migration of the Hellenide thrusting, which explains the palaeogeography of the Zakynthos basin. The diapiric movements of the Ionian Triassic evaporites regulated the configuration and the overall subsidence of the foreland basin and, therefore, the MSC expression in this area