Marlin are large, fast growing predators, as such, a high abundance of prey is required to sustain marlin fisheries. Unfortunately, in many regions of the world, lack of knowledge about marlin diet limits our capacity to protect essential prey stocks. Home to one of the world’s oldest recreational fisheries, the east coast of Australia is one such region. Little to no dietary research and the presence of commercial fisheries targeting small and mid-sized pelagic species threatens the east Australian marlin fishery. We assessed the diet of the three species targeted by the fishery, black (Istiompax indica), blue (Makaira nigricans) and striped (Kajikia audax) marlin, through stomach content analysis and DNA metabarcoding to identify species crucial to sustaining marlin. Overall, we found differences in the prey consumed by the three species: blue marlin primarily ate scombrids (tuna and mackerel) and flying squid; striped marlin primarily ate schooling species, both fish (such as oceanic pufferfish, scads and bigeyes) and cephalopods (argonauts and flying squid); black marlin primarily ate a variety of small coastal fish species (scad, mackerel, trevallies). Several deepwater species including lancetfish, swordfish and lanternfish were also present across the diet of all three species, though it is unclear if the marlin dive to feed on these or hunt them on the surface at night. Small pelagic fish and squid, but in particular small scombrids, particularly blue mackerel and skipjack, bullet and frigate tuna were key to the diet of all three species. Management should strive to maintain a relatively high biomass of these species to ensure enough prey to sustain the economically important recreational marlin fishery.