||Changes in the size distribution of zooplankton in the Humboldt Current System have been hypothesized to underlie observed changes in sardine and anchovy populations, the dominant pelagic fish species. To examine this hypothesis, the size distribution of over 15 000 zooplankton data samples collected since the 1960s was qualitatively determined. Dominance of each size group of zooplankton (small, medium and large) and of euphausiids was modelled using generalized additive models as a function of year, latitude, time of day, distance from the 200 m isobath (a surrogate for on-shelf versus off-shelf), sea surface temperature and salinity. The temporal (yr) pattern for euphausiid dominance was highly cross-correlated (i.e. was in phase) with the time series for estimated biomass of anchovy, and small zooplankton dominance with that for estimated sardine biomass. This supports the focal hypothesis based on feeding-energetic experiments, which showed energetic advantages to sardine filter feeding on smaller zooplankton and to anchovy bite feeding on larger copepods and euphausiids. Although euphausiids predominate offshore from the shelf break, anchovy biomass is generally highest on the shelf, suggesting a possible mismatch between anchovy feeding and euphausiid dominance. However, evidence concerning the offshore expansion of the anchovy range in cooler conditions, where both anchovy and euphausiids predominate, somewhat alleviates this apparent contradiction. A strong diel component to euphausiids and large zooplankton indicated diel migration for these zooplankton groups. That anchovy will preferentially eat euphausiids when they are more available (i.e. during the night and offshore) is supported by anchovy diet data.