The [MnO|SiO2,Al2O3,FeO,MgO] balanced ratio (i.e. the isometric log-ratio of the MnO concentration relative to the concentration of SiO2, Al2O3, FeO and MgO) of chlorite and of whole-rock composition is an effective discriminant between Mesozoic stratigraphic formations in the Magallanes Basin (Chile). The MnO content in chlorite is only controlled by the host rock chemistry and is dependent on the geological environment. The MnO content in chlorite remains unchanged at low-grade metamorphic conditions. Single-grain chlorite analysis (n = 1042, electron microprobe) and whole-rock analysis (n = 40, X-ray fluorescence) were used to discriminate stratigraphic formations and to decipher differences in the depositional environment in the Magallanes Basin. The samples are from one Upper Jurassic and three Cretaceous sedimentary units that were affected either by low-grade regional metamorphism or by Miocene contact metamorphism. The highest [MnO|SiO2,Al2O3,FeO,MgO] values are recorded in the upper Zapata Formation. The Punta Barrosa, Cerro Toro and Tobífera Formations show slightly lower [MnO|SiO2,Al2O3,FeO,MgO] values. Elevated [MnO|SiO2,Al2O3,FeO,MgO] values at the transition between Zapata and Punta Barrosa Formations record an oxygenated shallow marine environment that can be linked to the closure of the Rocas Verdes Basin and the onset of fold-and-thrust belt formation. Decreasing [MnO|SiO2,Al2O3,FeO,MgO] values from the Punta Barrosa towards the Cerro Toro Formation indicate gradually increasing water depths during the Upper Cretaceous that correlate well with the global sea level.