Resumen: Key aspects of the trophic ecology of small pelagic fish are not fully understood along the Humboldt Current. In this study, we examined the trophic seasonal dynamics, their relationships with oceanographic conditions, and interactions among cohabiting species (anchovy and common sardine) at the central (20°S) and southern (36°S) Humboldt Current System, using stable isotopes (δ13C, δ15N) measured at different levels of the food web (POM, copepods, and fish). Anchovies at both zones showed narrow δ13C seasonal variations but marked differences between zones. A wider inter-seasonal range in δ15N values, and a wider trophic amplitude (size of the isotopic niche) were observed in anchovies from the central HCS zone. In the south HCS, the trophic positions (TP) of both species showed slight variation during the year (TP anchovy: 3.15–3.43, TP common sardine: 3.08–3.28), with those of common sardine slightly lower than those of anchovy. However, the isotopic niche size in both species changed seasonally, as did the trophic overlap between them. Winter was when the lowest trophic overlap occurred between species, suggesting a trophic partitioning mechanism to overcome periods of reduced food availability. Overall, the seasonal variations of stable isotopes in the components of the food web seem closely associated with large-scale atmospheric and oceanographic processes (coastal upwelling) that affect both areas but with different intensity and duration during the year. Local geographic differences between zones also influence the input of organic carbon and nitrogen from certain sources, and interactions between species become significant during specific seasons.