Present-day Morocco constitutes the junction between the Atlantic and the Mediterranean domains. Its past evolution was driven by the development and the ultimate closure of the Tethys ocean. In order to constrain the evolution of the subsidence of this western part of the Tethyan margin, five regions of Morocco have been modelled, the Essaouira and Missour basins, the Middle and High Atlas and the High Plateaux. The subsidence history of these regions during the Triassic–Jurassic is linked to the evolution of the Atlantic and Tethyan oceans, from rifting to oceanic accretion. The subsidence history of the Essaouira Basin is the most directly linked to the evolution of the Atlantic Ocean. This basin records strong subsidence from Trias to Liassic time as well as a lesser pulse of subsidence during the Malm. After this time, the subsidence rate in the Essaouira Basin dramatically decreased and its present-day architecture was already acquired in the Upper Cretaceous, except for local uplifts. The Atlas intramarginal-rifted basins show strong subsidence at the beginning of the Lias, and a further episode of rapid subsidence during the Dogger. As soon as the alpine cycle started, topography resulting from tectonic inversion of the Atlas basins modified the pattern of sedimentary distribution, and the products of erosion were deposited in the border basins such as Missour, High Plateaux, Souss and Ouarzazate. The data available to us did not allow us to pinpoint the timing of the Atlas uplift between the Cretaceous and the Present, and we found no arguments to support the most likely Late Cretaceous/Tertiary age for the beginning of this uplift. Analysis of subsidence in the Missour Basin and in the High Plateaux confirms their permanent structural high position during Mesozoic time with respect to the High and Middle Atlas domains, and shows that these basins were individualised only after inversion of the Atlas region.