The efficient removal of nitrogen pollutants in the aquaculture systems is still a challenge due to the low concentration of organic carbon and high concentration of dissolved oxygen (DO) in the wastewater. The simultaneous partial nitrification, anammox and denitrification (SNAD) bioreactor was firstly used for the treatment of aquaculture wastewater in recirculating aquaculture system. The bioreactor operated for 180 days without adding extra organic carbon. After 60-day operation, the bioreactor reached the stable stage with the average concentration of ammonia/nitrate/nitrite/COD in the effluent with 0.26/0.75/0.47/0.27 mg/L. The Pseudoxanthomonas was the dominant genus in the biofilm samples. The typical nitrogen functional bacteria and genes for nitrification, anammox and denitrification were detected with different abundance in different procedures along the bioreactor. Network analysis revealed the significant correlations between nitrogen functional bacteria and genes. The SNAD bioreactor achieved the effective removal for nitrogen and COD under high DO conditions in recirculating aquaculture system.