Seismic near-vertical and undershooting experiments carried out in the southern upper Rhinegraben area between 1984 and 1991 show pronounced lateral variations of deep crustal properties. Significant differences in the apparent thickness of the reflective lower crust and the transparent upper crust appear to be related to different structural settings. A 12- to 14-km-thick reflective lower crust beneath a 15-km-thick transparent upper crust of the eastern graben shoulder (Black Forest) probably originated during Permo-Carboniferous reequilibration of thickened Variscan orogenic crust. Thinning of this lower crust by about 5 km beneath the graben and rifted domains transitional between graben and shoulder (the Dinkelberg block) is interpreted to be related to Cenozoic extensional faulting. A discrepancy between moderate extension of upper crust and lower crustal geometry indicates mechanical decoupling at depth during extension. Congruent modification of other physical properties is suggested by strong single reflective elements in the topmost parts of the thinned lower crust. In the transitional Dinkelberg block such an anomalously strong reflector occurs at a depth of 20 km below a pronounced local maximum of earthquake activity; it is interpreted to be the presently active zone of decoupling which in time shifted from the rift axis to the eastern transition area.