The recruitment rate of anchovy in the Peru-Chile upwelling system was studied by testing sensitive to environmental variability when the spawning stock is low in abundance. Times series of sea surface temperature, salinity, depth of the 15 °C isotherm, the upper limit of the oxygen minimum zone, upwelling indices, the Southern Oscillation Index, and indices El Niño 1+2 and El Niño 3.4 were summarized trough Principal Component Analysis (PCA). The first PCA (PC-I) explained 57% of variance and was related to interannual variability driven by the El Niño-Southern Oscillation. The second Principal Component explained 15% of variance and was linked to upwelling indices. Anchovy recruitment rate anomalies were correlated with PC-I scores on the basis of a 6-year-moving-window and accumulated correlation as time progressed. Significant correlation coefficients were found when the spawning stock biomass was low in abundance before 1990. Once sufficient spawning biomass was accumulated (after 1990), the stock was less sensitive to environmental variability. Thus, sensitivity to environmental changes in anchovy, and probably in other small pelagic fishes, is stock-size dependent. This is a key aspect to be considered in the management of transboundary fish stock shared between Chile and Peru, upon current efforts to develop an ecosystem approach to fisheries management. © 2013 Elsevier B.V.