Cyanobacteria sense the environmental phosphate level and respond accordingly with the help of a two component regulatory system SphS-SphR orthologous to PhoR-PhoB of E. coli, where SphS act as a sensor kinase and SphR as a response regulator. Under phosphate limiting condition SphS-SphR regulates the expression of many genes including genes which do not have the direct role in metabolism and transport of phosphate. Thus there is some crosstalk mechanism which connects this regulatory system to the other metabolic processes. Different types of enzymes and transporters are expressed by cyanobacteria under phosphate limitation to release and transport the phosphate from different organic compounds present in the environment. Genes encoding these enzymes and transporters contain Pho boxes in their promoter region where SphR binds and regulate their expression under phosphate limitation. The machinery and mechanism of regulation is not uniform in cyanobacteria as it varies in different groups according to their evolutionary adaptations. This review article is summarizing the reports on machinery and mechanism of organophosphate metabolism in cyanobacteria.