The discovering of anaerobic ammonium oxidation (anammox) process led to the development of autotrophic nitrogen removal systems for the treatment of effluents with low C:N rate. The anammox processes provide an efficient way to remove high concentrations of ammonium compounds from industrial and urban wastewater and covert them to dinitrogen. Nevertheless, recently obtained results suggest new ways for research on autotrophic nitrogen removal system including possibility for low temperature operation, adaptation to high organic matter loads and antibiotics inhibition effect. For these reasons, the prevalence and spatial distribution of anammox communities in autotrophic nitrogen removal wastewater treatment technologies, as well as their role in formation of fixed biofilms, are reviewed here in order to illustrate the present and future significance of these microorganisms in environmental biotechnology.