The objective of this research was to evaluate the nitrogen removal in a single stage rural wastewater treatment system. It was a modified subsurface vertical flow (SSVF) constructed wetland. The so-called Anaerobic Ammonium Oxidation(ANAMMOX) process is favored by imposing a saturated zone at the bottom of the basin. The nitrogen removal performances of this modified SSVF were compared to those of a conventional hybrid system where the well-known nitrification-denitrification process is performed. This study was carried out using three lab-scale pilots of constructed wetlands during four months: (1) a hybrid constructed wetlands with a reed-Phragmites australis SSVF bed in serial with a cattail-Typha angustofolia SSHF bed (SSVFp + SSHF). (2) A reed-Phragmites australis SSVF bed partially saturated at 40% of its depth (SSVFPS); (3) A cattail-Typha angustofolia SSVF bed partially saturated at 40% of its depth (SSVFTS). The results showed that the three configurations used in this study were efficient for most of the pollutants reduction. In fact, single-stage reactors have achieved similar chemical oxygen demand (COD) removal in comparison to the two-stage reactor independently of the macrophytes species. However, for Total Kjeldahl Nitrogen (TKN), a slightly higher nitrogen removal efficiency was recorded for (SSVF p + SSHF) with an average removal rate of 53% versus 48% and 51% for SSVF PS and SSVFTS respectively. These findings were highlighted with fluorescent in situ hybridization (FISH) analysis, which demonstrated the presence of major differences in the community composition and abundance of the bacteria involved with denitrification and nitrification in the three systems. In fact, SSVFP of the hybrid system was characterized by highest relative abundance of nitrifying bacteria (13% Nitrosomonas, 11% Nitrosospira, 14% Nitrospira and 10% Nitrobacter). While, the SSHF of hybrid system had larger number of denitrifying species than SSVF, with relative abundances of pseudomonas (3%), Paracoccus (9%), Zoogloea (6%), Thauera (4%), Thiobacillus (2%) and Aeromonas (1%). Interestingly, in the SSVFST (planted with Thypha angustofolia) where the relative abundance of nitrifying bacteria was very low (4% Nitrosomonas, 4% Nitrosospira, 4% Nitrospira and 1% Nitrobacter), we have detected the presence of ANAMMOX bacteria (3%). Accordingly SSVFST in the presence of Thypha angustofolia have favored the development of ANAMMOX activity in comparison to the other configurations.