Abstract:[Background] Stable partial nitritation is the bottleneck to achieve the anammox technology of municipal wastewater. At present, the effect of free nitrous acid (FNA) on the activity of nitrifying bacteria at home and abroad are mostly studied under aeration conditions, while not much research has been reported to discussed the effect of FNA on the activity of nitrifying bacteria under anoxic conditions. [Objective] To investigate the inhibitory effect of FNA on the activities of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB: Nitrospira and Nitrobacter) under aerobic and anoxic conditions. [Methods] The activities of AOB and NOB were investigated in a sequencing batch reactor (SBR) after FNA (initial concentration 1.16 mg/L) treatment under aerobic and anoxic conditions for 48?hours, based on the condition that the suspended solid concentration of mixed solution (MLSS) was 8?300 mg/L. [Results] After treatment under aerobic conditions with FNA for 48 hours, the FNA concentration was maintained at 1.16?1.17 mg/L, and the FA concentration was less than 0.017 mg/L after 48 hours, results showed that the abundance of AOB, Nitrospira and Nitrobacter did not change significantly; Compared with the blank group, the specific ammonia oxidation rate (rNH+ 4-N) and specific nitrite oxidation rate (rNO- 2-N) after aeration to 99 h decreased slightly, which decreased from 3.5 and 4.828?mg N/(g VSS·h) to 3.3 and 4.668 mg N/(g VSS·h) respectively, and the nitrite accumulation rate (NAR) was always lower than 33.2%. After treatment under anoxic conditions with FNA for 48 hours, the FNA concentration was maintained at 0.64?1.16 mg/L, and the FA concentration was lower than 0.039?mg/L, the AOB abundance changed slightly, while the Nitrospira and Nitrobacter abundance decreased significantly, which decreased from 3.002 9×109 and 4.245×108 copies/g VSS to 1.666 5×108 and 5.163?8×107 copies/g VSS, respectively; Compared with the blank group, the rNH+ 4-N decreased slightly, but the rNO- 2?N decreased significantly, which decreased from 4.828 mg N/(g VSS·h) to 0.007 mg N/(g VSS·h), and the NAR is maintained above 94% during over-aeration from 0 h to 292 h. [Conclusion] AOB and NOB were not significantly inhibited by FNA treatment for 48 hours under aeration conditions, but under anoxic conditions, NOB was strongly inhibited while AOB was slightly inhibited by FNA treatment for 48?hours, and stable partial nitrification could be achieved.