Cyanobacteria are widespread in eutrophic freshwater lakes and can produce potent toxins which pose serious risk for human and animal health, aquatic ecosystem sustainability and economic vitality. There are 9 major lakes, which eutrophication and related ecological problem had occurred in most of these lakes in Yunnan, China. In this study, water samples were collected at different sampling time from five freshwater plateau lakes, which located in the middle area of Yunnan province, to assess the cyanobacteria diversity vary with the seasons. The morphological character of cyanobacteria were observed by light microscope (LM), the genetic diversity of cyanobacteria had been demonstrated by constructed phylogenetic trees based on DNA sequence of cyanobacteria 16S-23S rRNA internal space (ITS).The results showed that a variety of cyanobacterial species were distributed in five plateau freshwater lakes. The cyanobacterial population consisted mainly of several Microcystis species as dominants in Dianchi Lake and the dominant species of cyanobacteria found in June to October of 2009 was Microcystis aeruginosa. The diversity of cyanobacteria in Caohai was higher than that of Waihai in Dianchi Lake.