Freshwater nitrification biofilter was domesticated to seawater nitrification biofilter by salinity gradient change method. Microbial community structure response to salinity domestication process was determined by denaturing gel gradient electrophoresis (DGGE) profiles of 16S rDNA V3 region. ATP contents were determined with luciferin-Luciferase mixtures method under different salinity impact.Resultsshowed that microbial community of the biofilm changed significantly before and after the salt change: the dominant species of fresh-water biofilm were Beta proteobacteria, and Delta proteobacteria; after the salt flush, the dominant species of the biofilter came into Stenotrophomonas of Gamma proteobacteria, Alpha proteobacteria, and Paenibacillus, etc. The biofilms’ ATP contents decreased by 17.4% (salinity 15) and 47.7% (salinity 25) after different salinity flush separately. In 25 ℃ biofilm cultivation condition, it takes 70 days to cultivate nitrifying biofilm in salinity 25 seawater; it takes 61 days that freshwater nitrifying biofilm domesticated directly for salinity 25 seawater nitrifying biofilm; it takes 56 days that freshwater nitrifying biofilm domesticated for salinity 10 seawater nitrifying biofilm firstly, then started for salinity 25 seawater nitrifying biofilm.