Seasonal change of microbial community including bacteria and algae in Tsukui Lake, an eutrophic reservoir in Kanagawa prefecture, was investigated by denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR) amplified fragments of 16S rDNA from May to October in 2000. A sudden algal bloom of cyanobacteria (Microcystis sp. and Anabaena sp.) after a heavy storm in July was observed both from a traditional algal cell counting and from a DGGE banding pattern analysis. In order to express graphically the seasonal change of the community based on the dissimilarity index, multi-dimensional scaling (MDS) was applied. The MDS map revealed a cyclic change of the community and a distinctive divergence from the path during the agal bloom. Since the divergence disappeared in an analysis with the DGGE image excluding the bands of cyanobacteria, the major part of the community appeared in the DGGE image might be independent of the sudden algal bloom. Dissimilarity of microbial communities was much lower among three different sampling sites than among the sampling months.