The role of zooplankton in microbial nitrogen turnover in marine environments is poorly understood. Here, we present results from two experiments designed to determine the excretion rate of ammonium and dissolved organic nitrogen (DON) by dominant copepods, Acartia tonsa and Paracalanus cf indicus, fed with two natural sized-fractioned diets (20–150 lm and < 20 lm), and its possible effects on the transcriptional activity of ammonia monooxygenase subunit A (amoA), a functional marker for ammonia-oxidizing archaea (AOA) and bacteria (AOB), as a response to the input of ammonium and DON by copepod excretion, during autumn and winter in central/southern Chile. Our results reveal that DON was the main excretion product, with rates up to 3.7 lmol L 21 h 21. DON production increased in copepods fed with the small-sized food. Ammonium was also excreted, with rates up to 0.08 lmol L 21 h 21 in autumn and 0.4 lmol L 21 h 21 in winter , and rapidly consumed by the microbial community, decreasing down to 0.07 lmol L 21 between the initial time to 4 h. Ammonium consumption coincided with increased AOB and AOA amoA transcript copies in copepods fed with the larger-sized food, while a different microbial community, probably heterotrophic, reacted to nitrogen input via excretion by copepods fed with the smaller-sized food in autumn. AOA-A was transcriptionally active in winter with nearly zero ammonium concentration, suggesting that AOA outcom-pete AOB when ammonium becomes limited. We conclude that nitrogen excreted by copepods can be used directly by microbial communities, including nitrifying ones. Zooplankton excretion may thus provide significant remineralized nitrogen for new and regenerated production in the upper ocean.