The Messianian Salinity Crisis refers to very large deposits of sea salt found in the Mediterranean region, about 1km below the current sea bed. (Named after Messina, a southern Italian city, where the deposits were first identified)

The salt deposits are around 50 times greater (at around a million cubic kilometres) than would be expected if the whole Mediterranean sea had evaporated at some stage.

The enormous quantities of salt are thought to have come from mutiple evaporation and refilling events of the Mediterranean basin. Probably around 500 million years ago.

Because the repeated filling episodes (from the Atlantic) would have cut extremely deep gorges - which are not present - the geological mechanisms are hard to explain. But various possible explanations have been put forward :

Several possible causes of the series of Messinian crises have been considered. While there is disagreement on all fronts, the most general consensus seems to agree that climate had a role in forcing the periodic filling and emptying of the basins, and that tectonic factors must have played a part in controlling the height of the sills restricting flow between the Atlantic and Mediterranean (Gargani and Rigollet, 2007). The magnitude and extent of these effects, however, is widely open to interpretation (see, e.g., van Dijk et al. (1998)

Source : Wikipedia

For technical details, see this research report in Nature volume 480, pages 359–363 ( a full copy of which may be found here )