The northern Humboldt Current system (NHCS) is the most productive eastern boundary upwelling system (EBUS) in terms of fish productivity despite having a moderate primary production compared with other EBUS. To understand this apparent paradox, an updated vision of the trophic relationships in the NHCS is required. Using δ13C and δ15N as a proxy of foraging habitat and trophic position, respectively, we focused on thirteen relevant taxonomic groups from zooplankton to air-breathing top predators collected off Peru from 2008 to 2011. Estimates of trophic position (TP) for the anchoveta Engraulis ringens were high (3.4–3.7), in accordance with previous studies showing zooplankton as a major contributor to anchoveta diet and challenging the often-cited short food chain hypothesis for this ecosystem. The squat lobster, Pleuroncodes monodon, a little studied consumer had similar δ15N values that of anchoveta, and thus similar trophic position. However, their differing δ13C values indicate that their foraging habitat do not fully overlap, which could alleviate potential competition between these species. Given the current high biomass of squat lobsters in the ecosystem, we encourage that future research focus on this species and its role in the diet of top predators. The present study provides first estimates of the relative TP of important taxonomic groups in the NHCS, which are needed to revisit anchoveta-centred ecosystem models for this region. Further work using amino acid compound specific stable isotope analyses is now required to confirm these TP estimates.