As a group of newly identified bioavailable phosphorus sources, phosphonates are an important part of the aquatic organophosphorus pool and constitute a key component in the phosphorus redox cycle. In recent years, dozens of cyanobacterial strains have been demonstrated to participate in the utilization and biosynthesis of phosphonates, aiding in the understanding of how these strains are able to adapt to low concentrations of phosphate. The discovery of cyanobacteria phosphonate utilization promotes our knowledge of cyanobacterial phosphorus strategy and water phosphorus cycle. Intensive studies have shown the duel ecological role of phosphonates that serve both as a source of phosphorus and as a biocide for planktonics in aquatic ecosystems. They can damage the aquatic ecosystems by driving a selective decrease in phosphonate-sensitive portions with a corresponding increase in phosphonate-consuming cyanobacteria. On the other hand, cyanobacterial methylphosphonate catabolism is regarded as a promising mechanism of oxic methane production in the water. This paper reviewed the research history of cyanobacterial phosphonates utilization and biosynthesis. A summary of the research progress on the ecological risks and ecological significance of cyanobacterial phosphonates metabolism was also provided. Finally, we proposed comments on the future focus in this field.