Biological nitrogen removal by using a co-culture of Anammox bacteria, ammonia-oxidizing archaea (AOA) and (ammonia-oxidizing bacteria) AOB microorganisms in a sequencing batch reactor (SBR) has previously been demonstrated experimentally. In this work, a mathematical model is developed to describe the microbial interaction among AOA, AOB and Anammox bacteria in the single-stage SBR and provide the first insights on the key role of AOA in such system. In this model, AOA and AOB jointly convert ammonium to nitrite partially, which provides electron acceptors to Anammox bacteria to oxidize the remaining ammonium forming dinitrogen gas. The model is successfully calibrated and validated using the long-term (around 350 days) dynamic experimental data from the SBR system, as well as two independent batch tests at different operational stages of the SBR. The model satisfactorily describes the nitrogen conversion data from the system. Modeling results show that AOA would outcompete AOB under low ammonium concentration and low dissolved oxygen conditions due to the revealed higher NH4+ affinity (K-NH4(AOA) of 0.06 g N m(-3)) and thus higher ammonia oxidation rate under oxygen-limited conditions, indicating that AOA could be a better partner to Anammox bacteria compared to AOB when treating low strength nitrogen sewage. The developed model could also predict and distinguish the different contributions of AOA and AOB to overall aerobic ammonia oxidizing potential, with more than 50% of ammonia oxidation being mediated by AOB at initial stage (similar to 300 days) and AOA being responsible for up to 90% of the ammonium removal afterwards. The results suggest AOA coupled with Anammox could provide new possibilities for biological nitrogen removal from low strength ammonium wastewater. (C) 2016 Elsevier Ltd. All rights reserved.