It is often assumed that variation in consumer stable isotope values (δ15N and δ13C) reflect shifts in diet between isotopically distinct prey species. However, an alternate hypothesis is that such variation could be as a result of spatial, temporal, or ontogenetic variation in the stable isotope values of a key prey species that propagate up marine food chains. In the Southern Ocean, Antarctic krill (Euphausia superba) occupy a key position, linking primary production to secondary consumers including fish, squid, seabirds, and marine mammals. As such Antarctic krill represent an ideal prey species to test the critical assumptions behind what has become a common method of dietary analysis in marine predators. Similar to previous studies, we found that stable isotope values of Antarctic krill exhibit significant intraspecific variation associated with both ontogenetic (size) and oceanographic factors (chlorophyll a concentration). Our modeling results showed that intraspecific variation in the stable isotope values of Antarctic krill has the potential to force mean isotope values of krill predators by as much as 2.4‰, independent of changes in the species composition of diet. Our findings indicate that intraspecific variation in the stable isotope values of a single, dominate prey species, such as Antarctic krill, has the potential to bias both absolute and relative estimates of marine predator diets using stable isotope mixing models. Therefore, caution is warranted to avoid spatial, temporal, and ontogenetic mismatches between the stable isotope values of prey sources used in mixing models and the actual stable isotope values of prey consumed by marine predators.