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Isotopic compositions of water of crystallization and sulfate anionic group in gypsum and polyhalite were used as tracers for events related to their formation and subsequent evolution, as for example origin of crystallization water and extent of thermal overprint. For this purpose, gypsum and polyhalite from the Permo-Triassic evaporites of the Eastern Alps, were analysed for isotope composition of sulfate anionic group (δ34S and δ18OSO4) and water of crystallization (δD and δ18O). For comparison, water of crystallisation of polyhalite samples of similar age from New Mexico (USA), Kłodawa (Poland) and Hattberg, Hesse (Germany) were also investigated. Estimated δ18O and δD values of polyhalite formation brines vary from 14.4 to 3.4‰ and 42.5 to −6.1‰, respectively. Gypsum formation brines show different δ18O and δD values, from −5.7 to −15‰ and −30.9 to −88.8‰, respectively. The measured δ18OSO4 values of sulfate group are compatible with a thermal overprint at 100°–200°C for both minerals. The thermal overprint documented for the Eastern Alps led to gypsum but not to polyhalite dehydration. The isotopic composition of water of crystallization suggests that polyhalite is preserving the isotopic signature of an enriched brine. During a subsequent event, anhydrite rehydrated to gypsum, with the isotopic composition of water of crystallisation indicating lower (δD and δ18O) values than the present-day meteoric water ones. Due to their distinct mineral structure and, as a result, different temperature of dehydratation, gypsum and polyhalite record different histories following precipitation in an evaporative system.