Abstract: In this study, a technique describing aquatic bacterial community structure has been developed by using restriction fragment length polymorphism of 16S ribosomal RNA gene(rDNA). The technique includes isolation of DNA directly from lake-water, amplification of rDNA using bacteria-specific primers, construction of plasmid library and digestion of randomly extracted recombinant plasmids with restriction endonuclease. The structure of bacterial community is determined using rDNA genotypes and their frequencies. This method has potentials in analyzing hidden genetic diversity of aquatic environments, tracing biological effectiveness of pollutants and evaluating environmental quality.