Late Permian to Triassic phases from the evaporite deposits of the Northern Calcareous Alps (NCA) and Central Alpine Mesozoic (CAM) were analysed for sulfur and oxygen isotope compositions. For the Upper Permian, most of the δ34S values are in the 11 to 12‰ range. Röt-type sulfates of Early Triassic age are characterized by a heavy sulfur isotopic composition of c. 26‰. The spatial compilation of the available data concerning the isotopic composition of Röt-type sulfates demonstrates that these evaporites are distributed over the entire area of the NCA. Their occurrences are associated with Early Triassic high-temperature conditions of the seawater and a widespread anoxia. The development of sulfates of Carnian–Norian age situated in the CAM is more modest; sulfates are characterized by a δ34S value of c. 15‰. The δ18O values show a broader distribution from 9 to 22‰, related to several factors such as type of deposit, recrystallization processes and bacterial sulfate reduction. The sulfate–sulfide thermometer applied to samples from NCA deposits indicates a thermal overprint of between 215 and 315°C. Microbeam measurements support zonation of minor elements in sphalerite. Sphalerite microstructure indicates thermal overprinting, with no microbial structure being preserved.