Abstract: With the aggravation of water eutrophication and continuing outbreak of cyanobacteria blooms, the harmful algal bloom could not only break the structure and the balance of hydrophy-tic ecosystem, but also pose serious health threats on animals and human due to cyanobacteria-toxin production. This paper reviews the progress of research on the secondary metabolites of cyanobacteria bloom toxins and cyanotoxin synthetase gene. The types of cyanotoxins, toxicology of cyanobacterial toxin, cyanotoxin synthetase gene and molecular biology identification for detecting the toxic cyanobacteria were described. Some suggestions on disadvantage of present research about cyanotoxin were put forward. The purpose of this review is to provide a theoretical basis and technological support on scientific evaluation of ecological and environment hazards of toxinproducing cyanobacteria and instituting earlywarning system of cyanotoxins.