Great Antarctic expeditions, and subsequently developed seal hunting and whaling industries left an enormous legacy in natural history museum collections. Stable isotopes of carbon delta13C and nitrogen delta15N from specimens preserved in the collections can provide valuable information on long-term changes in the foraging ecology of species and specify the baselines for future comparisons with modern samples. To provide the basis for analysing the impact of whaling on marine ecosystem structuring, we conducted the bulk isotope analysis from the specimens of baleen whales (Balaenoptera musculus and B. physalus), beaked whale (Berardius arnuxii), and seals (Arctocephalus australis and Hydrurga leptonyx) collected between 1843 and 1951, preserved in the collection of Natural History Museum, London. Having controlled for the Suess effect, delta13C values in B. musculus, B. physalus and H. leptonyx were different before and after the onset of industrial whaling (1904). Bone collagen delta15N values and corresponding trophic position consistently changed in B. musculus and A. australis, suggesting potential temporal shifts in their diets. This study highlights the use of museum specimens to trace the historical trends that could be associated with changes in the population structure and distribution of species and indicate long-term variability in their foraging ecology.