—Stable isotope ratios of carbon and nitrogen in archaeological and modern bone samples have been used to reconstruct the dietary changes of the South American sea lion Otaria flavescens from the late Holocene to the present in the southwestern Atlantic. We sampled bones from archaeological sites in northern-central and southern Patagonia, Argentina, and bones housed in modern scientific collections. Additionally, we analyzed the stable isotope ratios in ancient and modern shells of intertidal molluscs to explore changes in the isotope baseline and allow comparison between bone samples from different periods after correction for baseline shifts. Results confirmed the trophic plasticity of the South American sea lion, demonstrated the much larger impact of modern exploitation of marine resources as compared with that of hunter-gatherers, and underscored the dissimilarity between the past and modern niches of exploited species. These conclusions are supported by the rather stable diet of South American sea lions during several millennia of aboriginal exploitation, in both northern-central and southern Patagonia, and the dramatic increase in trophic level observed during the twentieth century. The recent increase in trophic level might be related to the smaller population size resulting from modern sealing and the resulting reduced intraspecific competition. These results demonstrate how much can be learned about the ecology of modern species thanks to retrospective studies beyond the current, anthropogenically modified setting where ecosystem structure is totally different from that in the pristine environments where current species evolved.