Autotrophic nitrogen removal systems have been implemented at full-scale and provide an efficient way for nitrogen removal from industrial and urban wastewaters. Our study present qualitative and quantitative analysis of archaeal and bacterial amoA genes and Candidatus Brocadiales bacteria analyzed in six full-scale autotrophic nitrogen removal bioreactors. The results showed that ammonium oxidizing bacteria (AOB) were detected in all bioreactors. However, ammonium oxidizing archaea (AOA) were detected only in the non-aerated technologies. Conversely, different Candidatus Brocadiales phylotypes appeared due to differences in influent wastewater composition and hydraulic retention time (HRT). In the same terms multivariate redundancy analysis confirmed that AOA was positively correlated with temperature, ammonium concentration and low HRT. However, AOB population was positively correlated with pH, temperature, and dissolved oxygen concentration. Our data suggested a correlation between the microorganisms involved in the nitrogen removal performance and the operational conditions in the different full-scale bioreactors. (c) 2017 American Institute of Chemical Engineers AIChE J, 64: 457-467, 2018