The study tended to disclose the evolutionary process of bacterial community that affected the performance of submerged membrane bioreactor (MBR) for aquaculture wastewater treatment via PCR amplification of 16S rRNA genes combined with denaturing gradient gel electrophoresis (DGGE) analysis. The selection pressure of gradually-increased salinity would worsen the treatment performance of MBR. CODMn removal rate slightly decreased from ca. 98.39% to 95.82%. Short-cut nitrification and denitrification (SND) phenomenon took place when salinity was ca. 21 g.L-1 and 28 g.L-1, respectively. Effluent NO2--N concentrations increased from 0.05 mg.L-1 to 1.05 mg.L-1 and reached to 2.66 mg.L-1 when salt concentration was 28 g.L-1. TN removal efficiency increased due to the SND process taking place in MBR. As the selection pressure of salt stress changed characteristics of community structures in the MBR, salt-tolerant microbe tended to gradually dominate in the population. Community-structure analysis indicated that Thiothrix eikelboomii, Pedomicrobium australicum, and Paracoccus bengalensis may hold crucial roles in the community ecology. Comparative PCR-DGGE analysis upon the mixed consortia in suspended activated sludge and cell-immobilized membrane revealed that there was no significant change of microbial structure taking place in the community. (C) 2013 Elsevier B.V. All rights reserved.