Cyanophages are viruses that exhibit a highly specific interaction mechanism with their host cyanobacteria. This specificity is driven by the recognition of host cell surface receptors by the phage tail fibers, which allows for the injection of the phage DNA into the host cell. Once inside the host cell, the phage DNA is replicated and transcribed, leading to the production of new phage particles. The evolutionary significance of cyanophages is multifaceted that lies in their role in shaping microbial communities and biogeochemical cycles in aquatic ecosystems. On one hand, cyanophages act as important regulators of cyanobacterial populations in aquatic ecosystems. These viruses have been shown to impact the growth, abundance, and diversity of cyanobacteria, which in turn can affect the functioning of the ecosystem as a whole. On the other hand, the study of cyanophages also provides insight into the coevolution of viruses and their hosts. The transfer of genetic material between cyanophages and cyanobacteria can occur through a variety of mechanisms, including lysogeny, transduction, and horizontal gene transfer. Understanding the mechanisms and evolutionary dynamics of virus–host interactions is therefore crucial for predicting the response of aquatic ecosystems to changing environmental conditions. Therefore cyanophages provide a window into the complex relationships between viruses and their hosts, and the important role of viruses in shaping aquatic ecosystems. Overall, this chapter presents valuable insights into the complex relationships between viruses and cyanobacteria, and the important role of viruses in shaping microbial communities and aquatic ecosystems.