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Scleractinian corals are the main framework-building groups in tropical coral reefs. In the coral holobiont, nitrogen-cycling mediated by microbes is fundamental for sustaining the coral reef ecosystems. However, little direct evidence characterizing the activities of microbial nitrogen removal via complete denitrification and anaerobic ammonium oxidation (anammox) in stony corals has been presented. In this study, multiple incubation experiments using 15N-tracer were conducted to identify and characterize N 2 production by denitrification and anammox in the stony coral Pocillopora damicornis. The rates of denitrification and anammox were recorded up to 0.765 ± 0.162 and 0.078 ± 0.009 nmol N 2 cm−2 h−1 respectively. Denitrification contributed the majority (∼90%) of N 2 production by microbial nitrogen removal in stony corals. The microbial nitrogen removal activities showed diel rhythms, which might correspond to photosynthetic oxygen production. The N 2 production rates of anammox and denitrification increased with incubation time. To the authors' knowledge, this study is the first to confirm and characterize the activities of complete denitrification and anammox in stony corals via stable isotope techniques. This study extends the understanding on nitrogen-cycling in coral reefs and how it participates in corals' resilience to environmental stressors. [Display omitted] • Anammox activity in stony corals is proved by isotope tracer for the first time. • Denitrification contributed ∼90% of N 2 production in stony corals. • Variations in anammox and denitrification in corals are significantly consistent. • Microbial nitrogen removal activity in stony corals shows diel rhythms. • Microbial nitrogen removal is influenced by coral photosynthetic oxygen production. [ABSTRACT FROM AUTHOR]