Museum collections not only provide educational tools for the public, but also reference material for osteological research and baseline information for understanding historical population dynamics and food webs. Such applications are only possible, however, with accurate identifications of museum osteological specimens, which is sometimes challenging, as specimens can be separated from their original information. In order to clarify missing information about provenience and species identifications, we analysed 13 historical whale bone specimens from the Museum of Zoology, Strasbourg, using a multidisciplinary approach that combined historical document analysis, osteology, and Zooarchaeology by Mass Spectrometry (ZooMS). These analyses enabled identification of elements from seven different whale species: five baleen whales (Mysticeti) and two toothed whales (Odontoceti). Two skeletons could be connected with letters from the early 1900s indicating they derived from whales stranded on the shores of South Island, New Zealand. One of these skeletons was digitized using a 3D scanner and can be freely viewed online. All of the samples will be available through a digital archive. The identification and digitization of these museum whale specimens, which include threatened and endangered whale species whose past histories are not yet fully understood, is of great value and ensures they are fully available for future systematic research. The study demonstrates a new and useful application of ZooMS, particularly in concert with other methods, to support museum collections research.