The pelagic thresher, Alopias pelagicus, plays a vital role in coastal and marine ecosystems as a top predator that feeds on species from low trophic levels. It is a commercial species relevant in Ecuador. The feeding chain of A. pelagicus was analyzed through carbon and nitrogen stable isotopes in the Southeast Pacific Ocean. Considering the lack of studies regarding this topic, this would elucidate the flow of nutrients and energy from the base up to this predator. Its diet composition included 19 prey species, out of which 10 were cephalopods and nine Osteichthyes. The most relevant species were the squid Ommastrephes bartramii, Dosidicus gigas, Stenoteuthis oualaniensis, and the fish Merluccius gayi peruanus. The pelagic thresher is a carnivore predator, and its prey species belong to tertiary and quaternary trophic levels. The carbon and nitrogen male isotopic ratios were similar to those of females, as were immature and mature organisms. This suggests that this species feeds in oceanic regions of low depths and could be exploiting and sharing an area with similar feeding resources. According to the mixing models, squids were the most important prey group, in which the squid Ommastrephes bartramii contributed most to its diet. Furthermore, this shark was characterized as a specialist predator with a trophic overlap by sex and maturity stages.