Ancient human-whale relationships are difficult to study because, counterintuitively, whales have been virtually invisible in the archaeological record despite the immense quantities of valuable products they provide. In this review, we explain the reasons for this invisibility, and we also show how an interdisciplinary approach combining archaeological and ethnographic studies with new biomolecular and isotopic techniques is yielding new insights, allowing a broader perspective on what whale bones found in archaeological sites or collections can tell us. Until recently, the rare whale bones found in archaeological sites were often overlooked or misidentified. The recent development of biomolecular methods, including ancient DNA analyses and collagen peptide mass fingerprinting (ZooMS), has enabled reliable identification of whale species from even small bone fragments. In addition, stable isotope analyses can provide information about ancient whale diets, feeding habits, migrations, or even environmental changes. Combined with radiocarbon dating, these approaches provide valuable ecological and historical context for whale conservation.