Stringent standards for nitrogen discharge necessitate the implementation of new systems for the sustainable removal of ammonium from wastewater. One of such systems is based on the process of anaerobic ammonium oxidation (Anammox), which is a new powerful tool especially for strong nitrogenous wastewaters. In this study, the Anammox process performance was tested with synthetic wastewater in a completely stirred tank reactor (CSTR). The reactor was operated for 511 days and fed with increasing amounts of ammonium and nitrite. In this period, an increase of ammonium and nitrite utilization rates were observed as a result of the increase of nitrogen loads in the influent. After 272 days, about 60% of the biomass was removed from the reactor and the system was restarted. Throughout 511 days 90% of the ammonium and more than 99% of the nitrite were converted mainly to dinitrogen (N2) and nitrate. The microbial community in the reactor was characterized with Fluorescence in situ Hybridization (FISH). The study showed that the population in the reactor was dominated by the deep-branching planctomycete Candidatus "Brocadia anammoxidans" strain Dokhaven 2.