This study investigated the influence of salinity and ammonium levels on ammonia-oxidizing bacteria (AOB) and archaea (AOA) by monitoring their amo subunit A (amoA) messenger RNA (mRNA) expression. The aerobic mini-continuous stirred-tank reactors (mini-CSTRs) were operated for 48 h under different salinity or ammonium levels. Quantification of archaeal and bacterial amoA mRNA levels using real-time reverse transcription polymerase chain reaction, combined with terminal restriction fragment length polymorphism (T-RFLP) analysis, was applied to investigate the differential transcriptional responses among AOA species. High salinity levels repressed both archaeal and bacterial amoA mRNA expressions. On the other hand, high ammonium levels repressed only archaeal mRNA expression, suggesting that ammonium is a significant environmental factor shaping abundance of AOA and AOB. T-RFLP results indicated that the impacts of salinity and ammonium levels were different among AOA species. Although further study is necessary to add significance to our findings, the combination of the short-term mini-CSTR operations and amoA mRNA-based analyses allow a preliminary study on the influences of environmental factors on competition between the AOA and AOB communities.