Large continental faults extend for thousands of kilometres to form boundaries between rigid tectonic blocks. These faults are associated with prominent topographic features and can produce large earthquakes. Here we show the first evidence of a major tectonic structure in its initial-stage, the Al-Idrissi Fault System (AIFS), in the Alboran Sea. Combining bathymetric and seismic reflection data, together with seismological analyses of the 2016 Mw 6.4 earthquake offshore Morocco – the largest event ever recorded in the area – we unveil a 3D geometry for the AIFS. We report evidence of left-lateral strike-slip displacement, characterise the fault segmentation and demonstrate that AIFS is the source of the 2016 events. The occurrence of the Mw 6.4 earthquake together with historical and instrumental events supports that the AIFS is currently growing through propagation and linkage of its segments. Thus, the AIFS provides a unique model of the inception and growth of a young plate boundary fault system.