The elevation of the intracontinental Atlas Mountains of Morocco and surrounding regions requires a mantle component of buoyancy, and there is consensus that this buoyancy results from an abnormally thin lithosphere. Lithospheric delamination under the Atlas Mountains and thermal erosion caused by upwelling mantle have each been suggested as thinning mechanisms. We use seismic tomography to image the upper mantle of Morocco. Our imaging resolves the location and shape of lithospheric cavities and of delaminated lithosphere ∼400 km beneath the Middle Atlas. We propose discontinuous delamination of an intrinsically unstable Atlas lithosphere, enabled by the presence of anomalously hot mantle, as a mechanism for producing the imaged structures. The Atlas lithosphere was made unstable by a combination of tectonic shortening and eclogite loading during Mesozoic rifting and Cenozoic magmatism. The presence of hot mantle sourced from regional upwellings in northern Africa or the Canary Islands enhanced the instability of this lithosphere. Flow around the retreating Alboran slab focused upwelling mantle under the Middle Atlas, which we infer to be the site of the most recent delamination. The Atlas Mountains of Morocco stand as an example of large-scale lithospheric loss in a mildly contractional orogen.