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The study of faunal remains from archaeological sites is often complicated by the presence of large numbers of highly fragmented, morphologically unidentifiable bones. In Australia, this is the combined result of harsh preservation conditions and frequent scavenging by marsupial carnivores. The collagen fingerprinting method known as zooarchaeology by mass spectrometry (ZooMS) offers the means to address these challenges and improve identification rates of fragmented bones. Here, we present novel ZooMS peptide markers for 24 extant marsupial and monotreme species that allow for genus-level distinctions between these species. We demonstrate the utility of these new peptide markers by using them to taxonomically identify bone fragments from a nineteenth-century colonial-era pearlshell fishery at Bandicoot Bay, Barrow Island. The suite of peptide biomarkers presented in this study, which focus on a range of ecologically and culturally important species have the potential to significantly amplify the zooarchaeological and paleontological record of Australia.