Abstract: Cyanophage is a double stranded DNA virus infecting cyanobacteria. It plays an important role in aquatic ecosystem, such as regulating abundance and diversity of cyanobacteria, algal physiological metabolism and element cycle. However, their abundance and genetic diversity in freshwater ecosystems are largely under estimated. To understand the diversity of cyanophage in different regions of Dianchi Lake and their correlation with environmental factors, the abundance and diversity of cyanophage in the surface water samples collected from northern（DCN） and southern（DCS） Dianchi Lake were investigated by using clone library and PCR technology. The clone library of cyanophage g20 gene include 182 sequences and 44 operational taxonomic units（OTU）（24 OTU from DCS and 20 OTU from DCN）, the diversity of cyanophage g20 gene was higher in DCS than in DCN. A phylogenetic analysis revealed that the 44 OTU were distributed in four major clusters（α, β, γ and ε）, with three unique subclusters（DC-Ⅰ, DC-Ⅱ and DC-Ⅲ）. Just 1 sequence in this study was closely related to the cyanophage g20 sequences from oceans（identity 67.96%）, the others were closely related to the cyanophage g20 sequences of freshwater（identity 70.56%～100.00%）. Principal co-ordinates analysis（PCoA） also showed that the cyanophage g20 sequences in this study were generally found to be more closely related to the cyanophage g20 sequences of freshwater than those from marine environments. Correlation analysis showed that the cyanophage g20 gene diversity was mainly negatively correlated with pH and chlorophyll a. The copy number of cyanophage g91 gene in Dianchi Lake was 4.462×10~6～2.596×10~7copies/mL, and the copy number of cyanophage g91 gene in DCN was significantly higher than that in DCS. The copy number of cyanophage g91 gene is negatively related to temperature and total nitrogen. The cyanophage in Lake Dianchi are abundant, and there are differences in the diversity and abundance of cyanophage in the DCN and DCS. The differences are correlation to pH, chlorophyll a, temperature, and total nitrogen.