New palynological data from the Sale brickyard (Atlantic coast of northern Morocco) are analyzed for their late Neogene biostratigraphical implications and the relationship with paleoenvironmental changes. Palynological zones (I to VI) described in this paper are based on palynomorph concentrations, fluctuations in species distribution, ratios between marine and continental palynomorphs, and the Last Appearance Datums (LADs) of twelve species. The brevity of some of the ranges in comparison with published dinoflagellates ranges from other locations is analyzed in view of important ecological events that took place in the Gibraltar Arc area at the end of the Miocene. Zone boundaries reflect global glacio-eustatic and/or local tectonic events that induced major modifications to the Atlantic/Mediterranean connections. The palynological data allow to differentiate time of eustatic versus tectonic control and permit to define how the paleoceanographic evolution of the Rifian Strait eventually led to the Messinian Salinity Crisis. We postulate that the nine LADs taking place at the Mio/Pliocene boundary results from the reconfiguration of oceanic circulation pattern and environmental conditions in the Gibraltar Strait area, as marine communication between the Atlantic Ocean and the Mediterranean Sea resumed, marking the end of the Messinian Salinity Crisis.