A new seismic data set was acquired using a dense temporary network of mobile seismic stations. It is combined with existing seismological data for the southern Rhine Graben. The data yielded some new focal mechanisms and allowed for a detailed local earthquake tomography. These methods give new insight in the structure of the crust and stress conditions in the area. By combining the tomography with the earthquake hypocenter locations and focal mechanisms, some of the structures in the P wave velocity model are interpreted as active faults. The eastern boundary fault zone of the graben is found to be activated in a left-lateral strike-slip sense. The southern continuation of these faults is formed by Variscan structures in the basement. A change in orientation of the graben axis between the main graben and its southern end have played a role during the development of the system. This difference in orientation caused the development of the Dannemarie and Allschwil subbasins during a late stage of the opening of the Rhine Graben. This study shows evidence for active faulting in the basement underneath the detachment of the Jura Mountains. These faults, which are interpreted as reactivated Permo-Carboniferous troughs, coincide with the frontal thrusts of the Jura Mountains. It might be that these structures in the basement have influence on the detachment tectonics in the region.