Abstract: Cyanobacteria are a kind of photosynthetic and oxygen-producing prokaryotic microorganisms which are widely spread in ocean, lake, paddy field, desert and even in some extremely adverse environments.Studying the genetic diversity of cyanobacteria is very important in understanding species evolution, exploitation and utilization of resources.In this paper, we reviewed the research progress on genetic diversity of cyanobacteria in marine, lake and paddy field based on molecular biological techniques.The distribution patterns of cyanobacteria and several unique cyanobacterial groups exist in different environments were summarized.Meanwhile, the effect of environmental factors on cyanobacterial diversity was discussed and several research problems and future research tendencies of cyanobacterial diversity study were proposed.