Juveniles of large hammerhead shark species occupy coastal nurseries before migrating offshore to reproduce. In the central Gulf of California, artisanal elasmobranch fisheries have reported catches of juvenile scalloped Sphyrna lewini and smooth S. zygaena hammerhead sharks, but their local foraging habits are yet to be fully understood. In this study, the trophic niches of both hammerhead species as well as of sympatric Pacific sharpnose sharks Rhizoprionodon longurio were investigated using stable isotope values (δ13C, δ34S and δ15N) and fatty acid compositions in whole blood and muscle tissues. Despite interspecific similarities among trophic niches, smooth hammerheads were characterized by lower δ13C, higher δ34S and greater proportion of docosahexaenoic acid (DHA) in both tissues, suggesting they were already partly relying on offshore pelagic resources. For scalloped hammerheads, muscle reflected coastal dietary resources, while offshore trophic markers were detected in blood integrating prey signal over shorter time periods, indicating their more recent initiation of ontogenetic migration. Multidimensional niche calculation revealed low overlap between hammerhead shark trophic niches, implying that potential fine-scale differences in habitat use could reduce competition between these morphologically and ecologically similar species. In the meantime, the isotopic niches of juvenile scalloped and smooth hammerheads were smaller than that of Pacific sharpnose sharks, suggesting they could be more specialized consumers. Overall, the identification of foraging grounds for juvenile hammerhead sharks calls for a future characterization of their residency time in coastal ecosystems to further understand their interactions with fishing pressure in the Gulf of California.