This study focuses on the comparative analysis of variables related to the trophic niche plasticity in the Galapagos sea lion (Zalophus wollebaeki). There is great concern regarding the future of this species, so study of the diet and the way these animals obtain their food is useful to understand and predict their survival possibilities in the long term. The combined use of scat analysis and stable isotopes helps to determine foraging habits of this species in greater detail. The objective of the study was to assess the feeding habits of Z. wollebaeki and its space–time variation. The scat analysis (n = 200) gave as a result space–time changes in the foraging strategies of this species. The isotopic values (n = 80) showed differences in relation to foraging grounds (δ13C: P = 0.001), but also suggested an apparent stability in the trophic level of their diet (δ15N: P = 0.084). These results constitute a relevant finding in the evolutionary behaviour of the species, showing that Z. wollebaeki has developed a high degree of plasticity in its foraging habits that may improve its survival in a highly demanding ecosystem in terms of limited and fluctuating resources.