Collagen is the dominant organic component of bone, a ubiquitous biomaterial that dominates the fossil and archaeological vertebrate record. The triple-helical structure of the collagen molecule enables it to intimately lock itself within the mineral phase of bone and these factors of stability, insolubility and high abundance makes it the most likely protein to be found in fossilised tissues. The interrogation of collagen via molecular methods such as soft-ionisation mass spectrometry provides an invaluable means of obtaining species identification in ancient bone, which unlocks whole proportions of vertebrate bone assemblages otherwise rendered useless in the absence of morphological characteristics. When investigating changes in faunal assemblages through time, the two vital pieces of information required are accurate species identification, and an accurate chronological framework. This research showcases a collagen fingerprinting technique, known as Zooarchaeology by Mass Spectrometry (ZooMS), as a pre-screening method for radiocarbon (14C) dating ancient bone, due to its ability to provide information on the presence and quality of collagen, the biomolecule from which a radiocarbon date can also be obtained. ZooMS is thereafter applied to hundreds of ancient bone samples from Cayman Brac (Cayman Islands) to determine faunal composition within the assemblage, and to report on its application in the establishment of a biodiversity 'catalogue' to showcase species presence and abundance throughout the zooarchaeological record. Within this remit, unique collagen fingerprints and sequences are disclosed for numerous extant and extinct vertebrates from the Cayman Islands; many endemic species of which have become extinct following human discovery of the islands just over 500 years before present. The research presented here interrogates the suitability of ZooMS as a tool to uncover documentation of ecological changes through time in this locality. As such, the application to identify bones that are suitable to be 14C dated and the successful taxonomic identification of hundreds of ancient bone samples demonstrates ZooMS as a valuable asset to understanding the key questions to how this ecosystem has changed with anthropogenic influence over time. The results carry the capacity to assist in the direct protection the ecosystems and habitats that are fundamental to the maintenance of high biodiversity on these islands and beyond. The insight that the Cayman Brac fossil record provides on our own species' impact on recent biodiversity might well inform future environmental policy on similar biomes to improve the global management of similarly threatened ecosystems.