Certain shark species are considered top predators, which bestows them with important roles in the trophic dynamics of marine ecosystems. The present study describes the ecology and ontogeny feeding of the shortfin mako shark Isurus oxyrinchus along Baja California Sur, Mexico, through stomach content analysis (SCA) and stable isotope analysis (SIA). A total of 272 stomachs and 39 muscle samples of I. oxyrinchus were analyzed. The SCA indicated that I. oxyrinchus has a wide trophic spectrum, with a consumption preference for Dosidicus gigas, Prionotus albirostris, and Scomber japonicus; however, feeding differences by sexes and sexual maturity stages were evidenced. The SCA indicated that I. oxyrinchus is a specialist consumer (Bi = 0.10) occupying high trophic positions (TP: 4.7–5.2). SIA reflected isotopic signals between –17.3 ‰ and –15.7 ‰ for δ13C and 15.5 ‰ and 19.5 ‰ for δ15N, but with some differences by maturity stages in δ15N (Young-of-the-year = 16.4 ± 0.66 ‰, Juveniles = 18.1 ± 0.13 ‰, adults = 18.3 ± 0.56 ‰). The SIA suggests that this species has a wide isotopic niche (SEAC: 1.08 ‰2) and occupies high TP (3.9–6.2). In conclusion, I. oxyrinchus presents segregation by sex and maturity stages, shows ontogenetic changes in habitat use and prey selection related to the physical characteristics of the zone (bathymetry), and plays important roles in the trophic dynamics of marine ecosystems.