The influence of salt (NaCl) on bacterial and archaeal communities in a submerged fixed bed bioreactor system treating urban wastewater with different saline concentrations was determined by 454 pyrosequencing. Cluster analysis of DGGE fingerprints showed significant differences of the community structure dependent upon the salt concentration applied to the influent. Proteobacteria was found to be the dominant Bacteria Phylum and Euryarchaeota was the main Archaea Phylum in all the experiments. While bacterial α-diversity decreased as salinity increased, the Archaea α-diversity was higher when the NaCl concentration in the influent rose. The differences found between the microbial communities and biodiversity showed that salinity had effects on the structure of microbial communities.