Fatty acids have been widely used as trophic biomarkers in marine mammals. However, for the South American sea lion, the most abundant otariid in the eastern South Pacific, there is no information about blubber fatty acids and their link to diet. Here, we compare fatty acid profiles of sea lions from two distinct oceanographic regions in northern and southern Chile. Their fatty acids vary greatly between regions, suggesting dietary differences at a spatial scale. The fatty acid C22:6ω3 was more abundant in sea lions from the northern region, likely associated with consumption of anchovy, cephalopods, and crustaceans, which are rich in that fatty acid, and have been reported as their main prey items. Sea lions from the southern region were richer in C22:1 and C20:1, characteristic of teleost fish, suggesting a piscivorous diet. Males displayed a more diverse fatty acid composition than females, suggesting a wider trophic niche. Few individual sea lions within the southern region had unusually high levels of C18:2ω6, commonly found in terrestrial environments. This suggests consumption of farmed salmon, whose diet is usually based on terrestrial sources. This demonstrates how human intervention is being reflected in the tissues of a top predator in a natural environment.