In Uruguay, the South American fur seal population (Arctocephalus australis) is increasing, whereas the South American sea lion (Otaria flavescens) population is declining. Previous research using fecal analysis suggested a high degree of trophic overlap between these species. In this study we used stable isotope analysis to assess whether trophic overlap occurs between female fur seals and sea lions during the breeding season. We measured delta N-15 and delta C-13 values in serum and skin from pups of both species (n = 47) to reflect pre- and postpartum maternal feeding habits, respectively. Our results suggested a lack of trophic overlap between lactating females; both serum and skin samples from sea lion pups had significantly greater delta C-13 and delta N-15 values than samples from fur seal pups, suggesting that lactating sea lions forage near shore, whereas lactating fur seals forage offshore. The pre- to postpartum diet shift in fur seals would be mainly caused by a reduction in the diversity of the exploited trophic levels, whereas in sea lions the shift could be related to a decrease in the diversity of foraging areas used. The observed trophic segregation between these sympatric otariids is probably driven by their synchronous breeding and similar maternal strategies.