Significance We reveal species-specific changes in penguin trophic responses to historic shifts in krill availability over the last century by applying new molecular isotope techniques to historic penguin museum specimens. Generalist foraging gentoo penguins, whose population increased 6-fold in the last 40 y, showed adaptive shifts in trophic position in concert with changes in Antarctic krill availability following historic exploitation of marine mammals and recent climate change. In contrast, chinstrap penguins maintained a consistent krill diet despite changes in krill availability and concurrent population declines. These results highlight how responses to shared environmental change can vary substantially among closely related species, supporting ecological niche theory that specialists will be more sensitive to environmental change than their generalist counterparts.