Post-collisional Upper Visean molasse sediments and magmatic rocks of the Badenweiler-Lenzkirch Zone reveal by microscopy of thin sections different degrees of hydrothermal illitization of feldspar and mica particles, and XRD, IR and XRF data of the <2 µm fractions show illitic material as the dominant clay mineral consisting of a mixture of 1M and 2M1 polytypes. Moreover, small amounts of illite/smectite mixed-layer minerals of R1-ordering are proved in the granites. In the separates, two illite mixing lines with different Fe + Mg contents are verified between authigenic illite from feldspar alteration and detrital illite in the molasse sediments, as well as between authigenic illite from feldspar alteration and altered mica flakes in the granites. Fe-rich detrital chlorite is present within the molasse sediments, while mixtures of high aluminous Fe-poor dioctahedral/di-trioctahedral chlorite with randomly interstratified chlorite/smectite mixed-layer minerals are formed from feldspar alteration in the granites. Illite K–Ar dating of the <2 and <0.63 µm fractions yields hydrothermal illitization of feldspar and partial resetting of the K–Ar system of detrital illite and mica flakes in the molasse sediments at ≥200 °C during Upper Permian to Middle Triassic times, while the granites in the eastern part of the study area were not altered contemporaneously. In contrast, hydrothermal activity at ≤200 °C during Upper Jurassic to Lower Cretaceous times occurred in the granites, whereas these temperatures were too low for resetting the older ‘Permo–Triassic’ illite K–Ar ages in the molasse rocks. Within both K–Ar age clusters, the data are seen to decrease with grain size and portion of illite 2M1 polytype. The alteration phenomena indicate multiple hydrothermal episodes in the study area, and they match those from the Central and Western European crust as fluid supply was controlled geodynamically by episodic break up of Pangea.