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The Southern Ocean is in an era of significant change. Historic overharvesting of marine mammals and recent climatic warming have cascading impacts on resource availability and, in turn, ecosystem structure and function. We examined trophic responses of sympatric chinstrap (Pygoscelis antarctica) and gentoo (Pygoscelis papua) penguins to nearly 100 y of shared environmental change in the Antarctic Peninsula region using compound-specific stable isotope analyses of museum specimens. A century ago, gentoo penguins fed almost exclusively on low-trophic level prey, such as krill, during the peak of historic overexploitation of marine mammals, which was hypothesized to have resulted in a krill surplus. In the last 40 y, gentoo penguin trophic position has increased a full level as krill declined in response to recent climate change, increased competition from recovering marine mammal populations, and the development of a commercial krill fishery. A shifting isotopic baseline supporting gentoo penguins suggests a concurrent increase in coastal productivity over this time. In contrast, chinstrap penguins exhibited no change in trophic position, despite variation in krill availability over the past century. The specialized foraging niche of chinstrap penguins likely renders them more sensitive to changes in krill availability, relative to gentoo penguins, as evinced by their declining population trends in the Antarctic Peninsula over the past 40 y. Over the next century, similarly divergent trophic and population responses are likely to occur among Antarctic krill predators if climate change and other anthropogenic impacts continue to favor generalist over specialist species.