Female northern elephant seals (Mirounga angustirostris) are migratory animals that form colonies along the coasts of California and the Baja California Peninsula, Mexico. A recent decline in abundance has been recorded in this species Mexican distribution, which is an important reason to investigate the different ecological processes operating in these colonies. The aim of this study was to determine values of stable isotope ratios (δ13C and δ15N) in pup fur as foraging maternal indicators. During the same breeding season (2015), pup fur samples were collected to investigate these foraging variations between the two major Mexican colonies—Guadalupe Island (GI) and the San Benito Archipelago (SBA). Isotopic areas were built using the ‘SIBER’ package in R, and a custom hierarchical Bayesian model was used to compare the values from both localities. Mean (± standard deviation [SD]) δ13C values for individuals from GI and the SBA were -16.9 ± 0.8‰ and -17.3 ± 0.4‰, respectively, while δ15N values were 17.4 ± 1.1‰ and 16.7 ± 1.1‰, respectively. The difference between the posterior means indicated a high probability (P > 99%) of GI having higher stable isotope ratio values than the SBA. For the posterior SDs, there were highly probable differences (P = 100%) only for δ13C, where GI had a higher dispersion. Such differences explained why GI presented a wider isotopic niche area than the SBA, indicating more diverse foraging habits along GI’s offshore-inshore gradient. Additionally, GI showed higher δ15N values than the SBA. Although this could be related to a slightly higher trophic position for GI individuals, the latitudinal effects of foraging grounds with distinct isotopic baselines remain a plausible explanation for the variations in both isotope ratios, suggesting that individuals from the SBA foraged in a more northerly location than those from GI. This study provides valuable knowledge about how females from both colonies partition resources, especially regarding habitat use.