We present a detailed analysis of the aftershocks of the May 21, 2003 Boumerdes earthquake (Mw = 6.9) recorded by 35 seismological stations and 2 OBS deployed in the epicentral area. This network recorded the aftershock activity for about 1 year and resulted in locating about 2500 events. The five main aftershocks (4.7 <M <5.8) display thrust faulting consistent with the main shock, except for the second event (M5.8, 29/05/2003) which depicts a strike-slip focal solution at the western tip of the rupture zone. Most aftershocks are clustered near the main rupture plane, in the footwall or at the westernmost tip of the 2003 Boumerdes rupture area. Many aftershocks last over the whole seismic crisis ahead (north) of the main rupture zone, forming a diffuse, low-angle surface within the footwall where the coseismic static stress change is predicted to increase. At the SW tip of the rupture, short-lived clusters locate at intersections of faults near the contact between the inner (Kabylia) and outer (Tell) zones. The tomographic inversion depicts high-velocity P- and S-wave anomalies coinciding with Miocene magmatic intrusive bodies in the upper crust, partially hidden by surrounding basins. The area of the main shock is associated with a large low-velocity body subdivided into sub-domains, including Neogene basins on land and offshore. Our results support a rupture model strongly controlled by geological inhomogeneities and extending as ramp–flat–ramp systems upward, favoring heterogeneous slip and segmentation in the fault plane with strong afterslip toward the surface. The diffuse aftershock activity in the footwall evidences an inherited discontinuity at mid-crustal depth that we interpret as the contact of Kabylian and African (Tethyan) continental crusts that were stacked during the Upper Miocene collision.