Abstract: Cyanophages, as a kind of peculiar viruse that infect specifically cyanobacteria, exists extensively in various aquatic environments. The gene psbA, encoding the D1 protein involved in photosynthesis reaction center, is a target gene of cyanophage, which not only reveals the genetic diversity of cyanophage, but also explores the relationship between the cyanophage and its host cyanobacteria. In this study, the plateau eutrophic Yilong Lake in Yunnan Province was taken as the research object. A total of 15 cyanophage psbA environmental sequences were obtained by using the psbA gene as a molecular marker from the concentrated water samples of Yilong Lake. Based on the cyanophage psbA sequence, phylogenetic tree was constructed, and the genetic diversity of cyanophage photosynthesis psbA gene in the water samples of Yilong Lake were analyzed. The results show that the psbA gene assemblage of the plateau eutrophic Yilong Lake in Yunnan Province are obviously different from those obtained from marine waters, other freshwater lakes and Japanese paddy floodwater.It is closer to evolutionary distance of paddy water in Northeast China, and the evolution is relatively independent. The novel psbA assembly of cyanophage was found in the plateau eutrophic Yilong Lake. For different seasons, the genetic diversity of psbA gene in cyanophage was more abundant in autumn.