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Constructed wetlands (CWs) have been widely applied in mariculture effluents disposal, however, the pollutants removal performance of mariculture wastewater with different salinity, especially the effect of different halophytes in CWs is rarely discussed. In this study, the nutrients removal efficiencies and absolute abundance of nitrogen (N) transformation microbes in CWs microcosms were investigated. With the increase of the salinity, both Phragmites australis (P. australis) and Suaeda salsa (S. salsa) planted CWs showed a significant reduction in chemical oxygen demand removal performance (p < 0.05), while no significant restriction on the nitrogen removal rates of all groups was obtained. The N removal efficiency was even promoted under 1.4% in these two kinds of CWs, respectively. And total phosphorus removal efficiency declined at the salinity of 1.4% and 2.1% for P. australis and S. salsa planted CWs, respectively. Further analysis showed that the presence of nitrification and denitrification was the major approaches of N removal. The absolute abundance of genes related with N transformation genes was significantly influenced by fluctuation of salinity, which affected the treatment efficiency of wastewater. The two different CWs presented high possibility of application on mariculture treatment in proper salinity.