The worldwide smallest cetacean, the vaquita (Phocoena sinus), is on the verge of extinction with fewer than 20 individuals left as of summer 2018. The main cause of mortality is bycatch by entanglement in illegal gillnets and environmental changes. Habitat disturbances have negatively impacted prey diversity, and therefore, the vaquita’s feeding success. We investigated the trophic niche of the vaquita and its variability from 1985 to 1993 by quantifying δ13C and δ15N values from bone samples (n = 33). We reconstructed part of vaquita’s refuge food web and identified some prey items. Between 1985 and 1993 the vaquita’s isotopic ellipses shifted moderately, δ13C and δ15N without significant differences, suggesting variations in habitat baseline values and probably prey composition. We observed a high overlap in the ellipses between males and females, suggesting that both sexes were feeding in the same geographic area over several years and with similar prey composition. Together, our results indicate that the vaquita is a generalist high-TL consumer, feeding on benthic and small pelagic prey it maintained similar mean δ15N values for years. Given these results, conservation efforts should intensify to protect the biodiversity of the Upper Gulf of California and the surviving vaquita.