Abstract: The rDNA 16S-23S intergehic spacer regions from Microcytis aeruginosa and Microcystis wesenbergii in Donghu Lake of China were sequenced and analyzedto illustrate the evolutionary affiliations between toxic and nontoxic strains in genus.The rDNA spacer sequences ranged from 360bp to 364bp exclusive of 16S and 23SrDNA coding regions, containing a Ile tRNA gene. Sequence comparisons bycomputer programs showed that distance values between two species were about 0.05,whereas distance values between two toxic strains of Microcystis aeruginosa (8641 and7820) were 0.04, which indicated Microcystis aeruginosa and Microcystiswesenbergiihas a quite close relationship. In addition, Sequence comparisons showed the variationsin the position 282-295bp were high between tWo species. High diversity of thisregion may facilitate the design of DNA probes specific for toxic Microcystis aeruginosa in Denghu Lake of China. It is the first sequence report of rDNA 16S-23Sintergenic spacer regions for Microrystis, and the sequences will serve as the basis forthe indepth studies on the phylogeny of Microcystis.