The crustal structure and topography of the Moho boundary beneath the Atlas Mountains of Morocco has been constrained by a controlled source, wide-angle seismic reflection transect: the SIMA experiment. This paper presents the first results of this project, consisting of an almost 700 km long, high-resolution seismic profile acquired from the Sahara craton across the High and the Middle Atlas and the Rif Mountains. The interpretation of this seismic data set is based on forward modeling by raytracing, and has resulted in a detailed crustal structure and velocity model for the Atlas Mountains. Results indicate that the High Atlas features a moderate crustal thickness, with the Moho located at a minimum depth of 35 km to the S and at around 31 km to the N, in the Middle Atlas. Upper crustal shortening is resolved at depth through a crustal root where the Saharan crust underthrusts the northern Moroccan crust. This feature defines a lower crust imbrication that, locally, places the Moho boundary at ~40–41 km depth in the northern part of the High Atlas. The P-wave velocity model is characterized by relatively low velocities, mostly in the lower crust and upper mantle, when compared to other active orogens and continental regions. These low deep crustal velocities together with other geophysical observables such as conductivity estimates derived from MT measurements, moderate Bouguer gravity anomaly, high heat flow, and surface exposures of recent alkaline volcanism lead to a model where partial melts are currently emplaced at deep crustal levels and in the upper mantle. The resulting model supports the existence of a mantle upwelling as mechanism that would contribute significantly to sustain the High Atlas topography. However, the detailed Moho geometry deduced in this work should lead to a revision of the exact geometry and position of this mantle feature and will require new modeling efforts.