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.