Understanding Palaeolithic hominin subsistence strategies requires the comprehensive taxonomic identifcation of faunal remains. The high fragmentation of Late Pleistocene faunal assemblages often... Show moreUnderstanding Palaeolithic hominin subsistence strategies requires the comprehensive taxonomic identifcation of faunal remains. The high fragmentation of Late Pleistocene faunal assemblages often prevents proper taxonomic identifcation based on bone morphology. It has been assumed that the morphologically unidentifable component of the faunal assemblage would refect the taxonomic abundances of the morphologically identifed portion. In this study, we analyse three faunal datasets covering the Middle to Upper Palaeolithic transition (MUPT) at Bacho Kiro Cave (Bulgaria) and Les Cottés and La Ferrassie (France) with the application of collagen type I peptide mass fngerprinting (ZooMS). Our results emphasise that the fragmented component of Palaeolithic bone assemblages can difer signifcantly from the morphologically identifable component. We obtain contrasting identifcation rates between taxa resulting in an overrepresentation of morphologically identifed reindeer (Rangifer tarandus) and an underrepresentation of aurochs/bison (Bos/Bison) and horse/European ass (Equus) at Les Cottés and La Ferrassie. Together with an increase in the relative diversity of the faunal composition, these results have implications for the interpretation of subsistence strategies during a period of possible interaction between Neanderthals and Homo sapiens in Europe. Furthermore, shifts in faunal community composition and in carnivore activity suggest a change in the interaction between humans and carnivores across the MUPT and indicate a possible diference in site use between Neanderthals and Homo sapiens. The combined use of traditional and biomolecular methods allows (zoo)archaeologists to tackle some of the methodological limits commonly faced during the morphological assessment of Palaeolithic bone assemblages. Show less