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Cyanobacteria are some of the oldest organisms known. Thanks to their photosynthetic apparatus, capable of splitting water into O-2, protons, and electrons, this large and morphologically diverse group of phototrophic prokaryotes transformed Earth’s atmosphere to one suitable for aerobic metabolism and complex life. The long debated Endosymbiotic Theory attributes to cyanobacteria also a significant role in the evolution of life, as important players in plastid origin of higher plants and other photosynthetic eukaryotes. Recent molecular surveys are trying to understand how, exactly, cyanobacteria contributed to plant genome evolution. Their ancient origin and their widespread distribution have recently opened the possibility of including fossil cyanobacterial DNA into the palaeo-reconstructions of various environments and in the calibration of historical records. Cyanobacteria occur in almost every habitat on Earth and can be found in environments subject to stressful conditions, such as desert soils, glaciers, and hot springs. They are common also in urban areas, where they are involved in biodeterioration phenomena. Their great adaptability and versatility are due to a characteristic cell structure, with typical inclusions and particular envelopes. They are the most complex prokaryotes, since they are able to form filaments, colonies, and mats, and they exhibit distinctive ways of movements. To live in different environments, facing biotic and abiotic stresses, cyanobacteria produce also a large array of metabolites, which have potential applications in several fields, such as nutrition, medicine, and agriculture. They have also an important ecological role, not only as primary producers, but also because of their coexistence (often, but not exclusively, in the form of symbiosis) with other organisms to which they supply nitrogen. On the other side, cyanobacteria can have also a negative impact both on the environment and society. In particular they can release a range of toxic compounds, cyanotoxins, diverse in structure and in their effects on human and animal health. In spite of their importance, cyanobacterial identification is not always easy and the use of modern methods (e.g., molecular sequencing, cytomorphology, and ecophysiology) has led to the revision of traditional taxa and to the discovery of new ones. Currently, the most accepted method for cyanobacterial classification is a polyphasic approach, also including comparison with reference specimens. Moreover, several authors are making efforts to create a unique nomenclature system for cyanobacteria.