ABSTRACT Denitrifying communities were detected in the water column of the Colombian Pacific Basin, with oxygen levels between 6 and 56 μΜ. They were analyzed by Terminal Restriction Fragment Length Polymorphism (TRFLP) of functional genes nitrite reductase (nirS) and nitrous oxide reductase (nosZ), and by pyrosequencing the gene nosZ. These genes are responsible for the production and consumption of the greenhouse gas N2O. The TRFLP analysis indicated that throughout the Colombia current, the composition of the nirS-type denitrifying community was more homogeneous than the nosZ-type community. The nosZ-type community presented the highest richness (up to 11 TRF) and diversity (Simpson Index 1/D = 4.85 and Shannon Index = 0.76) of terminal restriction fragments, as well as the higher richness of operational taxonomic units-OTUs (up to 71), obtained via pyrosequencing. Out of 84% of OTUs, 48% were assigned to the genus Pseudomonas, and 36% to environmental clones. These results indicate the presence of a nirS-community inhabiting the Colombian Pacific Basin, with low diversity and mostly restricted within 300 m depth. The nosZ- community showed similar richness and diversity of TRFs and OTUs to that reported for the South Pacific Ocean. These results demonstrate that although both denitrifying communities are present in the area, these communities differ in structure and dominance compared to previous reports for other denitrifying microorganisms.