In this study, the bacterial compositions of raw seawater and permeates from the conventional pre-treatment system and the membrane-based microfiltration system were examined during the seasons of autumn, winter and spring. The biofilm-forming potential was calculated based on the relative abundances of the putative biofilm-forming bacteria for the two seawater reverse osmosis pre-treatment systems. The cloning and sequencing analysis of the 16S rRNA gene reveals the dynamic shift in bacterial community structure to the genera capable of biofilm-formation through the pre-treatments. The highly diverse bacterial community structure of the raw seawater and the permeates hinders the statistical analysis for generalizing the bacterial components according to the sources or the seasons. This study proposes that the operational regimes of pre-treatment systems should be reconsidered based on the target bacterial groups of key biofilm formers. (C) 2013 Published by Elsevier B.V.