The reflooding of the Mediterranean Basin through the Gibraltar Strait (following the Messenian Salinity Crisis) characterizes an extreme event in the history of the Mediterranean. The Pliocene deposits of the Moroccan Mediterranean Coast provide invaluable sedimentary material for detecting the environmental and climatic conditions that accompanied this reflooding. In this context, we attempt to provide new insights into the modalities of Mediterranean reinundation based on the study of two key outcrops, one located in the western Mediterranean domain (Boudinar Basin, Northeastern Rif, Morocco) and the other in the Atlantic margin of the Rifian Corridor (Morocco). To contribute to this work, a preliminary palynological study of the sedimentary archives of the Oued Trifa section (Mediterranean domain), well-dated at high-resolution using planktonic foraminifera, has enabled us to reconstitute the marine and continental environments of the Zanclean (Lower Pliocene). In order to understand the spatial evolution of environments from the Atlantic to the Mediterranean during the Zanclean, we compared the results of this work with those already carried out in the Atlantic region, i.e., the continuous Upper Neogene sequence at Salé. The information on the marine environment deduced from the associations of planktonic foraminifera and dinocysts revealed a microfauna and microflora that were less abundant and less diversified in the Boudinar Basin and, conversely, in the Bou Regreg Valley. This reflects the openness of the marine environment on the Atlantic side. In both areas, the depositional environment is neritic. It is less distal and more epicontinental in the Boudinar Basin. Surface water conditions in the Atlantic domain are slightly cooler than in the Mediterranean. The Trifa section shows a significant increase in pollen and spores compared to dinocysts, while the Salé section indicates the opposite. Both sections are dominated by herbaceous species representative of open environments and a warm climate.