This study investigated the effect of salinity on ammonia-oxidizing archaea and bacteria (AOA and AOB) by operating two bioreactors under the salinity level of 2.5%o and 35%o, respectively. Both bioreactors achieved more than 95% of nitrification efficiency, but distinct AOA and AOB populations were enriched in the two bioreactors. For AOB, Nitrosomonas marina-like AOB and Nitrosomonas oligotropha-like AOB were dominated in high- and low-salinity bioreactors, respectively, while two different AOAs in marine group were dominated in high- and low-salinity bioreactors, respectively. The results from the amoA gene based real-time quantitative polymerase chain reaction indicated that, after 150 days of operation, AOA was more abundant than AOB by 1.6-54 and 2.3-81.1 times in the high and low salinity bioreactors, respectively. The results of inhibitory tests for seven chemicals on AOA-enriched sludge showed that 0.5 mg/L of phenol, benzene, toluene, and pyridine caused more than 55% of nitrification inhibition on AOA-enriched sludge. In comparison with AOB, AOA, however, showed higher tolerance to dimethyl sulfide and allylthiourea. Ethylenediamine presented a similar inhibitory effect on AOA and AOB.