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Abstract Cetacean remains are widespread in Japanese archaeology, yet their taxonomic identification is often limited. Here we investigate cetacean exploitation in northern Hokkaido through integrated zooarchaeological and palaeoproteomic analyses. We pursue two aims: (1) to improve cetacean Zooarchaeology by Mass Spectrometry (ZooMS) identifications by expanding reference markers; and (2) to reconstruct spatiotemporal patterns of cetacean use at Kafakai 1 (Okhotsk Period) and Onkoromanai (c. Epi-Jomon – Okhotsk period). We generated an expanded ZooMS reference set using LC–MS/MS-based collagen sequence reconstruction and MALDI–TOF peptide profiling, producing diagnostic markers for all extant baleen whale taxa and 49 odontocete taxa. ZooMS was then applied to 338 archaeological samples from Kafakai 1 and 26 from Onkoromanai, revealing at least twelve different species. At Kafakai 1, ZooMS indicates a persistent dominance of humpback whale throughout the sequence, with a late increase in pilot whale remains. In contrast, Onkoromanai shows comparatively higher representation of grey whale and includes bowhead whale, suggesting differences in cetacean availability and/or site function. Together, the assemblages support a model combining opportunistic use of large whale carcasses with targeted exploitation of small odontocetes, and highlight the value of expanded ZooMS reference datasets for reconstructing prehistoric human–cetacean relationships in the North Pacific.