Spatial or temporal isotopic variation, or both, in primary producers must be controlled for when investigating the foraging and trophic ecology of top consumers using isotopic data. Populations of the sister species Zalophus californianus and Z. wollebaeki are separated by approximately 3,350 km in the eastern tropical Pacific Ocean, which prevents contact and mixing between the 2 populations. To explore differences in trophic ecology between these species, as well as the impact of differences in baseline food-web isotope values between the 2 regions, we compared conventional dietary data derived from analyses of scat contents to isotopic values of hair collected from pups at 13 rookeries in the Gulf of California (Z. californianus) and 11 rookeries on the Galápagos Islands (Z. wollebaeki). Mean ± 1 SD δ¹³C and δ¹⁵N values were −15.9‰ ± 0.5‰ and 21.8 ± 0.7‰ in the Gulf of California, whereas for the Galápagos they were −14.5‰ ± 0.5‰ and 13.1‰ ± 0.5‰. Examination of scat data suggested overlap in 6 of the 10 most common prey consumed by sea lions. Trophic level (TL) derived from scat analysis was positively related with δ¹⁵N values for the Gulf of California rookeries, but estimates of TL for each region were similar (4.4 for Galápagos and 4.1 for Gulf of California), suggesting that foraging behavior makes a limited contribution to the large difference in δ¹⁵N value between the 2 populations. Particulate organic matter δ¹⁵N values near the Galápagos Islands are ∼5.3‰ lower than values in the Gulf of California, suggesting that the baseline food-web values account for approximately two-thirds of the observed difference in pup hair δ¹⁵N values. This study may provide clues to better understand isotopic values of marine top predators migrating across the eastern Pacific Ocean.