Denitrification, anammox (Anx) and di-nitrogen fixation were examined in two mangrove ecosystems- the anthropogenically influenced Divar and the relatively pristine Tuvem. Stratified sampling at 2 cm increments from 0 to 10 cm depth revealed denitrification as the main process of N sub(2) production in mangrove sediments. At Divar, denitrification was approx 3 times higher than at Tuvem with maximum activity of 224.51 + or -6.63 nmol N sub(2) g sup(−1) h sup(−1) at 0–2 cm. Denitrifying genes (nosZ) numbered up to 2×10 sup(7) copies g sup(−1) sediment and belonged to uncultured microorganisms clustering within Proteobacteria. Anammox was more prominent at deeper depths (8–10 cm) mainly in Divar with highest activity of 101.15 + or -87.73 nmol N sub(2) g sup(−1) h sup(−1) which was 5 times higher than at Tuvem. Di-nitrogen fixation was detected only at Tuvem with a maximum of 12.47 + or -8.36 nmol N sub(2) g sup(−1) h sup(−1). Thus, in these estuarine habitats prone to high nutrient input, N sub(2)-fixation is minimal and denitrification rather than Anx serves as an important mechanism for counteracting N loading.