Trophic competition among top predators is also influenced by environmental variability. However, the magnitude of the changes in contrasting events such as El Niño Southern Oscillation (ENSO) is poorly studied. The stomach contents of striped marlin (Kajikia audax), blue marlin (Makaira nigricans), and dolphinfish (Coryphaena hippurus) were analysed. We included the ENSO effect on the diet because we analysed organisms captured during 2010–2011 and 2014–2015, periods that, according to the Ocean Niño Index, were defined as the cold phase (CP) and warm phase (WP), respectively. Trophic diversity, feeding habits and strategy, trophic position (TP), trophic niche amplitude, and diet overlap were calculated. It was found that, despite a wide trophic spectrum, all three species were specialist predators in both phases. The most important prey species during both phases for striped marlin was Dosidicus gigas, while Auxis spp. was the most important prey of blue marlin. Dolphinfish fed mainly on Oxyporhamphus micropterus during the CP and Pleuroncodes planipes during the WP. Our results indicated that during both ENSO phases, all species maintained a trophic position similar to previous reports for the study area. However, for striped marlin, these differences were significant. Greater trophic competition was found during the CP (seven prey taxa shared) than in the WP (three prey taxa shared). These species often share the same environment, but their preference for feeding on different prey makes them occupy different trophic spaces, an aspect that allows their coexistence in time and space.