The Messinian Salinity Crisis in the Mediterranean, 5.96–5.33 Million years ago (Ma), represents the most recent case of massive evaporite deposition throughout an ocean basin. Here we quantitatively investigate the nature of the gypsum–marl cycles within its first phase, known as Lower Evaporites (LE) or Primary Lower Gypsum (PLG) (5.96–5.59 Ma). We conclude that to precondition the basin for deposition of the LE/PLG sequence, its connection with the open Atlantic must have been reduced to about 3% of the cross-sectional area of the modern Strait of Gibraltar. Using the modern strait morphology for scale, this would imply a connection with a depth of about 50 m and a width of several kilometres. We find that the LE/PLG evaporite–marl cycles may then have resulted from sea-level fluctuations of the order of 5 to 10 m and/or fluctuations in the Mediterranean's hydrological deficit of the order of 20%. Previous work has argued that sea-level control may be excluded, because there are too many cycles to agree with orbital obliquity-related timing. However, we argue from analogy with Quaternary sea- level records that sub-orbital sea-level fluctuations may easily reach the required magnitudes, so that sea-level control remains plausible.