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A gigantic cascade of Atlantic waters, filling the deep desiccated Mediterranean basin at the beginning of the Pliocene, has commonly been envisaged to end the Messinian Salinity Crisis (MSC). The Mediterranean lowstand during its final “Lago-Mare” phase, however, has long been subject to major controversy and has recently been seriously questioned again. Here, we present high-resolution ostracod distribution patterns of the MSC successions in the Black Sea basin (Zheleznyi Rog section; Russia) and the Mediterranean (Cuevas del Almanzora section; Spain) to study the origin and migration history of the Lago-Mare ostracods. We conclude that two major phases of faunal migration have taken place in the Messinian. The first phase corresponds to the Maeotian–Pontian boundary interval (~ 6.1–6.0 Ma) of the Paratethys, where mainly Pannonian species suddenly invaded the Black Sea region. The second migration event corresponds to the Lago-Mare phase of the Mediterranean when first (5.55–5.47 Ma) some opportunistic taxa (species of Cyprideis and Loxoconcha genera) and then (5.40–5.33 Ma) a more diverse assemblage of Paratethyan species occupied the entire Mediterranean region. The Spanish ostracod assemblages show a high percentage of Paratethyan (Pontian) ostracods, in agreement with previously studied Italian Lago-Mare sections. The similar palaeoenvironmental changes that developed roughly synchronously in the western and central Mediterranean marginal basins provide more evidence for intrabasinal exchange at high water level during the final stage of the Lago-Mare phase. This indicates that the Mediterranean in the latest Messinian was full of water (comparable to the present Caspian Sea) and that the Zanclean deluge, if happened, only surged some tens, up to few hundred metres, into the Mediterranean. [ABSTRACT FROM AUTHOR]