Bacteria are frequently studied in constructed wetlands (CWs) due to their effective involvement in pollutants purification processes. In this study, aerobic, anaerobic and total bacteria densities and their vertical distribution profile within pilot-scale vertical flow CWs planted with different plant species were investigated. Five beds were planted in monoculture with Andropogon gayanus, Chrysopogon zizanioides, Echinochloa pyramidalis, Pennisetum purpureum and Tripsacum laxum, and one unplanted bed was used as control. At the end of the treatment trial, bacteria were collected by taking cores of sediment samples at the corners and the center of each bed following six layers in the vertical profile. In fact, the presence of plants on CWs improved the bacterial density and removal efficiencies in the system, with yields from 5.9 to 24.1% regardless the pollutant. However, few anaerobic bacteria were obtained in the different wetlands, and unable to reduce NO3−, excluding for beds planted with T. laxum and P. purpureum. Besides, the number of aerobic bacteria determined decreased (i.e., 17.4 106 to 0.1 106 CFU.g− 1), while that of anaerobic bacteria increased (i.e., 0.1 106 to 2.1 106 CFU.g− 1) from the upper to the bottom layers in the planted beds. Otherwise, anaerobic bacteria were more abundant in the control than in planted beds. Then, total bacteria were dominated by aerobic bacteria, and decreased from surface toward the bottom. As P purpureum promotes the best performance, CWs with this type of plant could be a cost-effective alternative method of treating wastewater.