Fluorescence in situ hybridization (FISH) and quantitative PCR (q-PCR) analyses were performed to characterize the populations mediating ammonium oxidation processes in the oxic, suboxic and anoxic layers of the Cariaco Basin (Venezuela). To examine possible metabolic connections between nutrients and functional groups, distributions were compared to nutrient availability. Anaerobic ammonia-oxidizing bacteria (anammox), aerobic ammonia-oxidizing bacteria (AOB), and ammonia-oxidizing Archaea (AOA) were quantified within the water column. Two peaks in abundance of anammox bacteria were consistently observed during the three cruises that took place on December 8, 2010; May 6, 2011 and November 9, 2011 (C-175, C-180 and C-186). One peak was within the suboxic zone (up to 11,000 cells mL<super>-1</super>) and the other just below the suboxic zone in anoxic waters (up to 4,700 cells mL<super>-1</super>). This vertical separation observed in the anammox bacteria populations might be due to two different nitrite sources. The anammox bacteria population within the suboxic zone would be using the nitrite originated in the nitrification process. Anammox bacteria populations within the anoxic zone would be using the nitrite originated in the denitrification process. Of the anammox bacteria detected, 97% ?? 9% hybridized with the probe specific for the genus Scalindua. Aerobic ammonia-oxidizing bacteria and Archaea (Nitrosopumilus maritimus) exhibited abundance peaks in the lower oxic zone (up to 24,000 cells mL<super>-1</super>), at depths just above Anammox bacteria. Lower NH<sub>4</sub><super>+</super> concentrations correlated with increases in AOA and AOB abundances. Higher NO<sub>2</sub><super>-</super> and NO<sub>3</sub><super>-</super> concentrations correlated with enrichments in AOA and AOB, and lower NO<sub>2</sub><super>-</super> concentrations covaried with enrichments in Anammox. Estimated vertical fluxes of NH<sub>4</sub><super>+</super> and NO<sub>3</sub><super>-</super> were related to inventories of ammonia oxidizers, where lower NH<sub>4</sub><super>+</super> upward fluxes coincided with higher anammox bacteria inventories and higher NO<sub>3</sub><super>-</super> downward fluxes coincided with larger anammox bacteria, AOA and AOB inventories. This investigation demonstrates the presence of both aerobic and anaerobic ammonium oxidizers in the Cariaco Basin, suggests a metabolic relationship between anammox bacteria and AOB and AOA and, for the first time, examines the possible relations between these functional groups and ammonium and nitrate vertical fluxes.