Abstract: Cyanobacteria bloom is a global environmental issue, and the cyanotoxins produced by cyanobacteria seriously endanger aquatic ecosystem and human health. In order to analyze the genetic diversity of cyanotoxins synthesis genes of the toxin-producing cyanobacteria in Dianchi Lake, the expression and sequences of microcystin synthase gene mcyE, anatoxin synthase gene anaC and paralytic shellfish toxins sxtA gene were investigated by Polymerase Chain Reaction(PCR) and TA-cloning-sequencing in Haigeng from March 2017 to February 2018. These three genes were detected in all sampling area. Phylogenetic trees were conducted for analysing of these genes and it was found that the genetic diversity of the three cyanotoxins synthesis genes was relatively single, the mcyE gene was mainly produced by Microcystis, whereas anaC and sxtA genes were mainly produced by Aphanizomenon.