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Abstract. Diel vertical migration (DVM) can enhance the verticalflux of carbon (C), and so contributes to the functioning of the biologicalpump in the ocean. The magnitude and efficiency of this active transport ofC may depend on the size and taxonomic structure of the migrant zooplankton.However, the impact that a variable community structure can have onzooplankton-mediated downward C flux has not been properly addressed. Thistaxonomic effect may become critically important in highly productiveeastern boundary upwelling systems (EBUSs), where high levels of zooplanktonbiomass are found in the coastal zone and are composed by a diverse communitywith variable DVM behavior. In these systems, presence of a subsurfaceoxygen minimum zone (OMZ) can impose an additional constraint to verticalmigration and so influence the downward C export. Here, we address theseissues based on a vertically stratified zooplankton sampling at threestations off northern Chile (20–30∘ S) duringNovember–December 2015. Automated analysis of zooplankton composition andtaxa-structured biomass allowed us to estimate daily migrant biomass by taxaand their amplitude of migration. We found that a higher biomass aggregatesabove the oxycline, associated with more oxygenated surface waters and thiswas more evident upon a more intense OMZ. Some taxonomic groups, however,were found closely associated with the OMZ. Most taxa were able to performDVM in the upwelling zone withstanding severe hypoxia. Also, strongmigrants, such as eucalanid copepods and euphausiids, can exhibit a largemigration amplitude (∼500 m), remaining either temporarily orpermanently within the core of the OMZ and thus contributing to the releaseof C below the thermocline. Our estimates of DVM-mediated C flux suggestedthat a mean migrant biomass of ca. 958 mg C m−2 d−1 may contributewith about 71.3 mg C m−2 d−1 to the OMZ system through respiration,mortality and C excretion at depth, accounting for ca. 4 % of the netprimary production, and so implies the existence of an efficient mechanismto incorporate freshly produced C into the OMZ. This downward C fluxmediated by zooplankton is however spatially variable and mostly dependenton the taxonomic structure due to variable migration amplitude and DVMbehavior.