Coastal wetlands, as transient links from terrestrial to marine environments, are important for nitrogen removal by denitrification. Denitrification strongly depends on both the presence of emergent plants and the denitrifier communities selected by different plant species. In this study, the effects of vegetation and habitat heterogeneity on the community of denitrifying bacteria were investigated in nine coastal wetlands in two preserved areas of Spain. Sampling locations were selected to cover a range of salinity (0.81 to 31.3 mS/cm) and nitrate concentrations (0.1 to 303 μM NO3-), allowing the evaluation of environmental variables that select for denitrifier communities in the rhizosphere of Phragmites sp., Ruppia sp., and Paspalum sp. Potential nitrate reduction rates were found to be dependent on the sampling time and plant species and related to the denitrifiercommunity structure, which was assessed by terminal restriction fragment length polymorphism analysis of the functional genes nirS, nirK and nosZ. The results showed that denitrifier community structure was also governed by plant species and salinity, with significant influences of other variables, such as sampling time and location. Ruppia sp. and Phragmites sp. selected for certain communities, whereas this was not the case for Paspalum sp. The plant species effect was strongest on nirK-type denitrifiers, whereas water carbon content was a significant factor defining the structure of the nosZ-harboring community. The differences recognized using the three functional gene markers indicated that different drivers act on denitrifying populations capable of complete denitrification, compared to the overall denitrifier community. This finding may have implications for emissions of the greenhouse gas nitrous oxide