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In many oceanic regions, growth of phytoplankton is nitrogen-limited because fixation of N₂ cannot make up for the removal of fixed inorganic nitrogen (NH⁺₄, NO^-₂, and NO^-₃) by anaerobic microbial processes. Globally, 30-50% of the total nitrogen loss occurs in oxygen-minimum zones (OMZs) and is commonly attributed to denitrification (reduction of nitrate to N₂ by heterotrophic bacteria). Here, we show that instead, the anammox process (the anaerobic oxidation of ammonium by nitrite to yield N₂) is mainly responsible for nitrogen loss in the OMZ waters of one of the most productive regions of the world ocean, the Benguela upwelling system. Our in situ experiments indicate that nitrate is not directly converted to N₂ by heterotrophic denitrification in the suboxic zone. In the Benguela system, nutrient profiles, anammox rates, abundances of anammox cells, and specific biomarker lipids indicate that anammox …