The base compositions of DNAs from nine Microcystis strains, as determined by high-performance liquid chromatography, were 41 to 42 mol% G+C. Chromosomal DNAs derived from these strains were found to be extremely resistant to many restriction endonucleases, and a restriction analysis revealed the presence of a dam-like methylase or both dam-and dcm-like methylases in all of the strains examined. Genomic Southern hybridization in which a synthetic oligonucleotide probe (rpoD probe) was used showed that members of the genus Microcystis might have multiple rpoD homologs, and the hybridization signal patterns observed with the DNAs of Microcystis aeruginosu strains were different from each other.Members of the genus Microcystis are unicellular colonyforming cyanobacteria (blue-green algae) which produce surface blooms in eutrophic water; some strains have been found to possess a peptide toxin, microcystin (13,19). The taxonomy of Microcystis species traditionally has been based on colony morphology and cell arrangement (10). However, these morphological features are easily changed in culture (16). Rippka proposed that, as prokaryotes, cyanobacteria are divisible into five major groups (sections) on the basis of culture characteristics (16), and Microcystis strains have been classified as members of the Microcystis cluster of the genus Synechocystis (26). At the present time, data for chemical, genetic, and physiological characteristics based on the use of axenic cultures are required for the taxonomy of cyanobacteria. The importance of G+ C contents in microbial classification has been established. However, the data available on the G + C contents of Microcystis clones are limited. Chromosomal DNAs from different filamentous and unicellular cyanobacteria have been shown to be surprisingly resistant to cleavage by a number of restriction endoriucleases (5, 11,15). This resistance could be due to the absence of specific sequences or to modification (methylation). Resistance of Microcystis DNAs to restriction endonuclease cleavage has been little examined. RNA polymerase holoenzymes contain the principal sigma factors that play a central role in the initiation of transcription (12). l'anaka et al. designed a synthetic oligonucleotide probe ( p o D probe) from an amino acid stretch conserved among the principal sigma factors in Escherichia coli and Bacillus subtilis (24) and, using it, detected four or five signals from the DNAs of Anabaena sp. strain PCC 7120, Synechococcus sp. strain PCC 7942, and Synechocystis sp. strain PCC 6803 by genomic Southern hybridization (23). Recently, we developed a technique for isolating axenic clones of Microcysti3 by using a combination of the agarose plate technique and two-step centrifugation and isolated nine axenic Microcystis clones (13,18,19). In this paper we describe the G+C contents, restriction endonuclease cleavage characteristics, and multiple rpoD homologs of the DNAs of Microcystis isolates.Cultures. Axenic Microcystis aeruginosa strains K-17, * Corresponding author.K-79,...