The Middle Eocene oil shale deposits of Messel are famous for their exceptionally well-preserved, articulated 47-Myr-old vertebrate fossils that often still display soft tissue preservation. The isotopic compositions (O, C, Sr, Nd) were analysed from skeletal remains of Messel's terrestrial and aquatic vertebrates to determine the condition of geochemical preservation. Authigenic phosphate minerals and siderite were also analysed to characterise the isotope compositions of diagenetic phases. In Messel, diagenetic end member values of the volcanically-influenced and (due to methanogenesis) 12C-depleted anoxic bottom water of the meromictic Eocene maar lake are isotopically very distinct from in vivo bioapatite values of terrestrial vertebrates. This unique taphonomic setting allows the assessment of the geochemical preservation of the vertebrate fossils. A combined multi-isotope approach demonstrates that enamel of fossil vertebrates from Messel is geochemically exceptionally well-preserved and still contains near-in vivo C, O, Sr and possibly even Nd isotope compositions while bone and dentine are diagenetically altered.Enamel of the hippomorph perissodactyl Propalaeotherium has low δ13C values (−9±0.7‰), typical for C3-plant-feeders. Dentine of the same teeth has δ13C values 15–17‰ higher, amongst the highest δ13Cbioapatite values reported for terrestrial vertebrates. This reflects diagenetic carbonate exchange with the strongly 12C-depleted anoxic lake bottom water. Enamel 87Sr/86Sr values (~0.711±0.001) are consistent with Propalaeotherium feeding on Palaeozoic bedrocks surrounding Lake Messel and suggests that the basaltic tuff ring around the maar was already eroded 640ka after its formation. Dentine has, however, much lower, volcanically influenced 87Sr/86Sr (~0.706) due to diagenetic Sr uptake from the lake water/oil shale. Enamel δ18Op values (~18±0.6‰) of Propalaeotherium are 2–3‰ lower than those of bones and scales of aquatic vertebrates that lived in the 18O-enriched lake water. Using transfer functions, a δ18OH2O value of −5±1‰ for meteoric water and a MAT of ~18±2.5°C were reconstructed for Messel.