Nitrogen removal communities performing wastewater treatment consist of ammonia oxidisers, nitrite oxidisers, denitrifiers, and anammox bacteria, and the proportion and activity of particular microbial groups depend not only on the physiochemical parameters of the bioreactor, but also on the composition of the inoculum. Nitrifiers and denitrifiers usually dominate in conventional wastewater treatment systems due to the fact that nitrification and denitrification are the most commonly used nitrogen removal processes. However, from the economical point of view in case of wastewater with high ammonia concentrations, anammox-based technologies are desirable for their treatment. The disadvantage of such systems is slow anammox bacteria growth, which extends an effective technological start-up. Thus, in this study, a fast start-up of the anammox process supported with an anammox-rich inoculum was performed in a sequencing batch reactor (SBR). Using anammox inoculation of SBR laboratory system, the start-up can be fastened to 85 days with 84.5% of nitrogen removal efficacy. The spatial distribution of nitrogen removal bacteria analysed with fluorescent in situ hybridisation revealed that anammox and nitrifiers are located side by side in the flocs and the relative number of ammonia and nitrite oxidisers decreased after 85 days of the experiment.