The Messinian salinity crisis (also referred to as the Messinian event, and in its latest stage as the Lago Mare event) was an event in which the Mediterranean Sea went into a cycle of partial or nearly complete desiccation (drying-up) throughout the latter part of the Messinian age of the Miocene epoch, from 5.96 to 5.33 Ma (million years ago). It ended with the Zanclean flood, when the Atlantic reclaimed the basin.

Sediment samples from below the deep seafloor of the Mediterranean Sea, which include evaporite minerals, soils, and fossil plants, show that the precursor of the Strait of Gibraltar closed about 5.96 million years ago, sealing the Mediterranean off from the Atlantic. This resulted in a period of partial desiccation of the Mediterranean Sea, the first of several such periods during the late Miocene. After the strait closed for the last time around 5.6 Ma, the region's generally dry climate at the time dried the Mediterranean basin out nearly completely within a thousand years. This massive desiccation left a deep dry basin, reaching 3 to 5 km (1.9 to 3.1 mi) deep below normal sea level, with a few hypersaline pockets similar to today's Dead Sea. Then, around 5.5 Ma, wetter climatic conditions resulted in the basin receiving more fresh water from rivers, progressively filling and diluting the hypersaline lakes into larger pockets of brackish water (much like today's Caspian Sea). The Messinian salinity crisis ended with the Strait of Gibraltar finally reopening 5.33 Ma, when the Atlantic rapidly filled up the Mediterranean basin in what is known as the Zanclean flood.

Even today, the Mediterranean is considerably saltier than the North Atlantic, owing to its near isolation by the Strait of Gibraltar and its high rate of evaporation. If the Strait of Gibraltar closes again (which is likely to happen in the near future in geological time), the Mediterranean would mostly evaporate in about a thousand years, after which continued northward movement of Africa may obliterate the Mediterranean altogether.

Only the inflow of Atlantic water maintains the present Mediterranean level. When that was shut off sometime between 6.5 to 6 MYBP, net evaporative loss set in at the rate of around 3,300 cubic kilometres yearly. At that rate, the 3.7 million cubic kilometres of water in the basin would dry up in scarcely more than a thousand years, leaving an extensive layer of salt some tens of metres thick and raising global sea level about 12 metres.

In the 19th century, the Swiss geologist and paleontologist Karl Mayer-Eymar (1826–1907) studied fossils embedded between gypsum-bearing, brackish, and freshwater sediment layers, and identified them as having been deposited just before the end of the Miocene Epoch. In 1867, he named the period the Messinian after the city of Messina in Sicily, Italy. Since then, several other salt-rich and gypsum-rich evaporite layers throughout the Mediterranean region have been dated to the same period.

Seismic surveying of the Mediterranean basin in 1961 revealed a geological feature some 100–200 m (330–660 ft) below the seafloor. This feature, dubbed the M reflector, closely followed the contours of the present seafloor, suggesting that it was laid down evenly and consistently at some point in the past. The origin of this layer was largely interpreted as related to salt deposition. However, different interpretations were proposed for the age of salt and its deposition.

Earlier suggestions from Denizot in 1952 and Ruggieri in 1967 proposed that this layer was of Late Miocene age, and the same Ruggieri coined the term Messinian salinity crisis.

New and high-quality seismic data on the M-reflector were acquired in the Mediterranean Basin in 1970. At the same time, the salt was cored during Leg 13 of the Deep Sea Drilling Project conducted from the Glomar Challenger under the supervision of co-chief scientists William B. F. Ryan and Kenneth Hsu. These deposits were dated and interpreted for the first time as deep-basin products of the Messinian salinity crisis.