Abstract: Microcystis strains isolated from bloom-forming ponds were analyzed based on gvpA-C intergenic sequence and 16S rDNA. Several gvpA-C intergenic sequences shared an 172—176 bp extra sequence. An alignment of different types of 0.27 kb sequences, exclusive of the extra sequence, showed over 50 substitutions, whereas in a 0.69 kb hot spot region of 16S rDNA only 8 substitutions were identified. Compared to 16S rDNA, the gvpA-C intergenic sequence was generated by one-step PCR without contamination from co-existing bacteria and showed much higher variability, therefore should be useful in typing of Microcystis. Due to horizontal gene transfer, the two sets of types demonstrated an intersecting relationship. In addition, Microcystis gvpA-C intergenic sequences with or without the extra sequence formed two distinct clusters in a phylogenetic tree.