Harbour seals (Phoca vitulina) and northern elephant seals (Mirounga angustirostris) are the only phocid species found in Mexico. There is evidence that harbour seals at other latitudes exhibit non-migratory behaviour; however, there is lack of knowledge regarding this species' movements in Mexico. In contrast, elephant seal migrations to high latitudes are documented. In order to analyse this behaviour in harbour seals, hair samples (N = 19) were collected from weaned, or nearly weaned, pups on Natividad Island, Baja California (BC), during the 2013 breeding season (February). Lanugo samples (N = 20) were also collected from elephant seal pups on the San Benito Archipelago (60 km north of Natividad) during the same season, providing information on maternal foraging during the last 4–5 months before sampling. Of the two species, BC harbour seals had higher isotope values, reflecting their non-migratory behaviour. These differences may be due to the depleted base values in the higher latitude foraging areas used by northern elephant seals relative to the areas around Natividad frequented by harbour seals. A lower trophic position by elephant seals was considered but taken as an unlikely explanation for this variation. Bayesian analysis confirmed the distinction, with a low overlap value (0.4) and different isotopic spaces (Phoca: 0.5, Mirounga: 1.6). Building upon previous studies of the trophic ecology of the two phocids that inhabit the region, we provide new information by comparing the two species during the same season using the same tissue type sampled from individuals of similar age classes.