AbstractClupeiform fishes are ecologically and economically important species contributing to industrial and artisanal fisheries worldwide. They represent key links in food webs, influencing the dynamic between trophic levels. The dietary interactions of these species are poorly studied in many regions, yet essential for fisheries management. To elucidate the role of these species in food webs of the Southern Brazilian Bight pelagic fisheries, we used metabarcoding analysis of fish stomach contents of Clupeiformes and possible predators. Onboard sampling from March to September 2016 allowed for processing of 87 stomach samples representing 31 species (including 12 samples representing three species of Clupeiformes). Links between trophic levels showed the predominance of Sardinella brasiliensis and Engraulis anchoita as important dietary items of a large range of fishes (28 species belonging to 18 families) and representing the majority of the total prey read abundance assigned to clupeiform fishes (~46% and ~32%, respectively). Opisthonema oglinum contributed to the diet of 16 species in 13 families and ~18% of total read abundance of clupeiform fishes as prey. The appearance of multiple clupeiform taxa in the diet of predators that are not commonly associated with pelagic prey indicates that ecosystem‐based fisheries management should not be separated between pelagic and demersal fisheries. The diet of Clupeiformes revealed an unexpectedly large diversity of fish species and a low proportion of invertebrates (<5% of clupeiform prey reads). This was likely due to a combination of both a limitation of the metabarcoding method (primer bias and low success of invertebrate taxonomic identification) as well as a contribution of early life stages (ichthyoplankton) to the diet of these fishes. The potential role of clupeiform fish populations as a constraint to the recruitment from the ichthyoplanktonic phase of other ecologically or commercially important fishes should be considered as an important direction for future studies.