The Messinian Salinity Crisis is well known to have resulted from a significant drop of the Mediterranean sea level. Considering both onshore and offshore observations, the subsequent reflooding is generally thought to have been very sudden. We present here offshore seismic evidence from the Gulf of Lions and re‐visited onshore data from Italy and Turkey that lead to a new concept of a two‐step reflooding of the Mediterranean Basin after the Messinian Salinity Crisis. The refilling was first moderate and relatively slow accompanied by transgressive ravinement, and later on very rapid, preserving the subaerial Messinian Erosional Surface. The amplitude of these two successive rises of sea level has been estimated at ≤500 m for the first rise and 600–900 m for the second rise. Evaporites from the central Mediterranean basins appear to have been deposited principally at the beginning of the first step of reflooding. After the second step, which preceeded the Zanclean Global Stratotype Section and Point, successive connections with the Paratethyan Dacic Basin, then the Adriatic foredeep, and finally the Euxinian Basin occurred, as a consequence of the continued global rise in sea level. A complex morphology with sills and sub‐basins led to diachronous events such as the so‐called ‘Lago Mare’.This study helps to distinguish events that were synchronous over the entire Mediterranean realm, such as the two‐step reflooding, from those that were more local and diachronous. In addition, the shoreline that marks the transition between these two steps of reflooding in the Provence Basin provides a remarkable palaeogeographical marker for subsidence studies.

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The Paril Formation (South Pirin and Slavyanka Mountains, southwestern Bulgaria) and the Prodromos Formation (Orvilos and Menikion Mountains, northern Greece) consist of breccia and olistostrome built up predominantly of marble fragments from the Precambrian Dobrostan Marble Formation (Bulgaria) and its equivalent Bos-Dag Marble Formation (Greece). The breccia and olistostrome are interbedded with thin layers of calcarenites (with occasional marble pebbles), siltstones, sandstones and limestones. The Paril and Prodromos formations unconformably cover the Precambrian marbles, and are themselves covered unconformably by Miocene and Pliocene sediments (Nevrokop Formation). The rocks of the Paril Formation are intruded by the Palaeogene (Late Eocene–Early Oligocene) Teshovo granitoid pluton, and are deformed and preserved in the two limbs of a Palaeogene anticline cored by the Teshovo pluton (Teshovo anticline). The Palaeocene–Middle Eocene age of the formations is based on these contact relations, and on occasional finds of Tertiary pollen, as well as on correlations with similar formations of the Laki (Kroumovgrad) Group throughout the Rhodope region.The presence of Palaeogene sediments within the pre-Palaeogene Pirin–Pangaion structural zone invalidates the concept of a ‘Rhodope metamorphic core complex’ that supposedly has undergone Palaeogene amphibolite-facies regional metamorphism, and afterwards has been exhumed by rapid crustal extension in Late Oligocene–Miocene times along a regional detachment surface. Other Palaeogene formations of pre-Priabonian (Middle Eocene and/or Bartonian) or earliest Priabonian age occur at the base of the Palaeogene sections in the Mesta graben complex (Dobrinishka Formation) and the Padesh basin (Souhostrel and Komatinitsa formations). The deposition of coarse continental sediments grading into marine formations (Laki or Kroumovgrad Group) in the Rhodope region at the beginning of the Palaeogene Period marks the first intense fragmentation of the mid- to late Cretaceous orogen, in particular, of the thickened body of the Morava-Rhodope structural zone situated to the south of the Srednogorie zone. The Srednogorie zone itself was folded and uplifted in Late Cretaceous time, thus dividing Palaeocene–Middle Eocene flysch of the Louda Kamchiya trough to the north, from the newly formed East Rhodope–West Thrace depression to the south.

The Terminal Eocene global cooling Event created a substantial sea-level drop. This caused biological extinctions and allowed for large scale dispersal events (e.g. European Grande-Coupure, Mongolian Remodelling). Originating from Asia, the first western European ruminant appeared during this dispersal and climatic event, correlated with the Eocene-Oligocene boundary. A second wave composed by Bachitheriidae and Tragulidae arrived in Europe 2 Myr later. The origins of this diachronism have remained unknown until now. Here we describe the first ante-Grande-Coupure ruminant from Europe, found in the Late Eocene of Bulgaria (south-eastern Europe). We ascribe it to Bachitherium patriarcha nov. sp. which predates its western European relatives by at least 4.5 Myr; the specimen possesses the most primitive dental morphology known in the family. During the entire Eocene and until the early Oligocene (ca. 31 Ma), southeastern Europe remained isolated from the rest of Europe by the Paratethys sea. Early Oligocene orogenic events restored dryland conditions and enabled the arrival of Bachitherium in Western Europe (herein named "Bachitherium event"). However, none of the abundant perissodactyl fauna from southeastern Europe migrated to Western Europe during this time, because, like their relatives in Central Asia, they did not survive the Terminal Eocene cooling and aridity event.