A pilot-plant to desalinate seawater using reverse osmosis membrane has been in operation for 1.7 years. Two different pretreatment systems, the conventional process with sand-filtration and the membrane-based process of microfiltration with 0.6 mu m pore size, have been used. Besides the physical, chemical, and economic indices needed to evaluate the efficiency of the pretreatment systems, the microbial community structure should be analyzed in order to ensure the removal of bio-foulants, marine biofilm-forming bacteria. In this study, the removal of biofilm-forming bacteria by two seawater reverse osmosis (SWRO) pretreatment systems was qualitatively evaluated through the construction of a 16 S rRNA gene library. The relative abundance of certain member of gamma-proteobacteria, which are responsible for the major pioneering activity in the formation of biofilms by adhesion to surfaces in the marine environment, was calculated. Raw seawater was dominated by biofilm-forming bacteria of Alteromonas (39.2%), Cowellia (7.6%), and Glaciecola (43.0%) genera. The bacterial diversity was significantly changed by the conventional pretreatment system, while microfiltration had little effect on the diversity. The conventional pretreatment system maintained the dominance of biofilm-forming bacteria, but the sum of the relative abundance of biofilm-forming bacteria was decreased from 79.8% to 50.0%. By decreasing the dominance to only 10.0%, microfiltration showed an efficiency superior to that of the conventional pretreatment system for the removal of biofilm-forming bacteria. (C) 2011 Published by Elsevier B.V.