Abstract: In order to investigate the genetic diversity and distribution of g20 gene of cyanophages among different eutrophic plateau lakes in Yunnan Province, water samples were collected from Dianchi Lake, Xingyun Lake and Fuxian Lake. The phylogenetic tree was constructed to analyze the phylogenetic diversity of cyanophage g20 genes in the autumn and winter of 2018. A total of 43 g20 genes of cyanophage were cloned and sequenced. Phylogenetic analysis show that the distribution of cyanophage g20 genes in water samples of these lakes was closely related to those in other lakes and oceans, but far from those in paddy water. Between autumn and winter, the genetic diversity of g20 genes among the lakes was not significantly different. The genetic diversity of the cyanophage g20 genes of the three plateau lakes in Yunnan province is relatively rich, and novel groups of g20 genes are existing.