Biofoulants by autopsy of RO membrane and microbiological quality of the intake water were investigated with the samples obtained from existing RO desalination plant. The analysis of organic matters of the biofilm on the membrane surface showed that macromolecular substances such as proteins and carbohydrates were the major composites and contributed to the biofilm formation. Comparison of microbial communities between the RO membrane and seawater intake samples revealed that alpha-proteobacteria was the most abundant bacterial group both in the membrane surface and the intake water, and the phylum Firmicute and Planctomycetes, which were proposed not to be originated from the seawater intake, appeared as the potential biofoulants target. The final goal of this research project is to develop a rapid and sensitive biosensor system to detect the problematic biofoulants on RO system in seawater desalination process, with the tool of fluorescence nanoparticles. Preliminary result of this study showed that RO biofouling was contributed both by microbial cells and the extra organic substances and these identification and sensing of specific biofoulant targets will be beneficial to process efficiency