This study focused on the investigation of the Archaeal communities in three autotrophic nitrogen removal (anammox) full-scale bioreactors located in The Netherlands (Apeldoorn, Rotterdam and Olburgen) designed with different configurations and technologies: partial nitritation-anammox (2 step), CANON and DEMON. qPCR and 16S rRNA gene tag-pyrosequencing were used to analyze the abundance and composition of the Archaeal communities in the different bioreactors. Recent reports have pointed the potential involvement of nitrifying Archaea and methanogens in anammox based processes. qPCR results demonstrated the presence of Archaea in these three bioreactors in ratios higher than 0.3% relative abundance with respect to total prokaryotic community. Pyrosequencing data and phylogenetic analysis revealed the presence of several organisms phylogenetically related to Archaea previously reported as involved in biofilm formation and methane and nitrogen cycles, like Methanosaeta sp., Methanosarcina sp. and Methanobrevibacter sp. Our results confirmed the presence of Archaeal populations in autotrophic denitrification systems (anammox processes) at full-scale plants. Pearson coefficient analysis showed an inverse significant correlation between Archaeal populations and efficiency of the bioreactors studied. The putative roles of these anammox-associated Archaeal communities are discussed.