The preservation of fossils over long periods of geological history usually has special characteristics, and the specific conditions for successful fossilization have not been established yet. Triassic bones from SW China are characterized by an exceptionally broad variation in the style of preservation. This region presents a perfect natural lab for the study of conditions advantageous for bone preservation. Twenty-five specimens of marine reptiles from the Middle to Late Triassic black shales were sampled and examined in petrographic thin sections, by Raman spectroscopy and wavelength-dispersive X-ray spectroscopy. Our results revealed evidence that the bones were heated, possibly by hydrothermal fluids or by regional geological events, and we observed fluorite in fossil bone for the first time. We discriminate five stages of bone alteration: 1) no alteration beyond diagenetic mineral precipitation in the bone porosity; 2) weak alteration of apatite and migration of kerogen from the shale into the fossil bone; 3) formation of authigenic fluorite needles; 4) Recrystallization of bone apatite to idiomorphic apatite while bone structure is still present; 5) complete loss of bone structure and replacement by idiomorphic apatite. Systematic carbon Raman thermometry returns temperatures up to 150-180°C, indicating that loss of histological information might be linked to temperatures near to low-grade metamorphism. This study provides reference data for different stages of bone alteration, which is important for the study of bone diagenetic processes in dependence of higher than near-surface temperatures.