Warming increases the metabolic rates of fishes and drives their oxygen demands above environmental oxygen supply, leading to declines in fish growth and smaller population sizes. Given the wide variability in species' sensitivity to changing temperature and oxygen levels, warming and oxygen limitation may be altering the composition of fish communities and hence, that of fisheries catches. Here, we test the hypothesis that changing temperatures shape the composition of pelagic fisheries catches in the Eastern Tropical Pacific. We expect that under warmer conditions, pelagic fisheries catches will be dominated by tropical species with higher oxygen demands and less surplus oxygen for growth. To test this hypothesis, we combined an index of the physiological vulnerability of exploited large pelagic fishes (e.g. tuna and billfish) to changing ocean temperatures and oxygen levels with fisheries catch data from 1970 to 2016. We found that warming is the main driver of changes in the physiological performance and catch composition of this fishery, and that oxygen limitation may be causing a significant breakpoint in the relationship between sea surface oxygen and the index of vulnerability of pelagic catches in the Ecuador and Galapagos Exclusive Economic Zones. Warm temperature anomalies due to El Niño were projected to cause reductions in the physiological performance of large pelagic fishes, although this only led to changes in catch composition during the extremely warm events. Our results suggest that catches are vulnerable to future warming, as the increasing frequency, duration and magnitude of marine heatwaves associated with climate change impact catch composition.