Migrant biomass and carbon fux of vertically migrating meso- and macrozooplankton was calculated for shelf (< 200 m bottom depth) and oceanic (> 200 m bottom depth) regions in the northern Benguela upwelling system. Active carbon fux is based on migrant biomass and respiration rates. Especially in upwelling regions, oxygen minimum zones (OMZ) are a common feature and thus the impact of low oxygen concentrations (i.e. hypoxia) on metabolic rates also should be considered. Copepods were sampled with a 0.25 m2 multiple opening and closing net (Multinet midi), while a larger net (1 m MOCNESS) was used for the collection of euphausiids and decapods. Copepods were dominant in the upper 50 m of shelf areas with a migrant biomass between 23 and 47 mg C m-2, whereas euphausiids were more abundant at oceanic regions with up to 1437 mg C m-2. Decapods were absent at the shelf but important in greater depth at oceanic stations (> 150 mg C m-2). Mass-specifc respiration rates of individuals from the OMZ were reduced by 46-64% as compared to metabolic rates of specimens from surface waters. The resulting active carbon fux out of the upper 100 m by vertically migrating species was estimated with 4.3 mg C m-2 d-1 for shelf regions and 11.2 mg C m-2 d-1 for oceanic areas, which is equivalent to 4% and 35% of sinking POC, respectively. These data emphasize the crucial role of the OMZ for future developments of realistic carbon budgets under climate change scenarios.