The semi-permanent coastal upwelling system within the Humboldt Current System (HCS) off northern Chile provides nutrient-rich, oxygen-poor water to the euphotic zone that contributes to high levels of primary production and restricts the vertical distribution of most zooplankton species according to their tolerance to hypoxia within this highly heterogeneous environment. The day/night vertical distributions of two calanoid copepods, Eucalanus inermis and Nannocalanus minor, were studied concerning the presence of oxygen-poor water associated with the Oxygen minimum zone (OMZ) at a coastal and an offshore station off northern Chile (~20°S), by stratified sampling from the surface to a depth of 600 m. At the coastal station, most of the population of both species remained above the OMZ, whereas at the offshore station, most populations remained at the edge of the OMZ. Both species exhibited reverse diel vertical migration between day and night and were positively correlated with dissolved oxygen and chlorophyll-a, suggesting that both species may prefer oxygenated waters and avoid the OMZ. However, E. inermis and N. minor exhibited distinct behavior, with E. inermis displaying significant variations among stations and strata and N. minor showing differences only among strata, particularly in the upper strata where it was more aggregated. The results helped us understand the behavior and distribution of zooplankton related to OMZ and how they may change as ocean temperature increases worldwide.