Cyanophages play an important role in the evolution of cyanobacteria. They control cyanobacterium abundance, population dynamics, and the structure of natural communities. Cyanophages are a global reservoir of genetic information. They act as vectors that transfer genes, endow cyanobacteria with novel properties, and affect the rate and direction of evolutionary processes. Lysogeny makes a significant contribution to the maintenance of the gene pool and ecological adaptation of cyanobacteria. The integration of many cyanobacterial genes into cyanophage genomes indicates that a genetic transfer occurs between hosts and phages. Such a gene transfer performs the driving functions in adaptive microevolution. Analysis of the molecular base of cyanophage–host interactions strongly supports the concept of the coevolution of cyanophages and cyanobacterial genomes.