The first microorganisms that carried out the photosynthesis process were cyanobacteria, and together with the production of oxygen, they changed the composition of the atmosphere. Today they have increased their abundance globally, due to changes in the use of water bodies, producing phenomena called cyanobacterial blooms, often accompanied by toxins such as anatoxins, saxitoxins, microcystins, hepatotoxic, neurotoxins and lipopolysaccharides, which is known as harmful algal blooms, resulting in environmental and public health problems depending on the species that inhabits or predominates in the aquatic system in Chile. The general objective was to propose cyanobacteria as bioindicators of eutrophication and to generate a record for each species present in water bodies in the central-southern zone of Chile. For this purpose, cyanobacteria species were identified through a polyphasic approach, and information was collected on the environmental conditions in which the blooms occurred. The results were a total of 15 species, 5 species of cyanobacteria identified polyphasically, 9 species identified morphologically, 1 through molecular analysis and the collection of optimal environmental conditions, in addition to synthesizing the results in a cyanobacteria card. With this card, the water quality can be determined according to the species that inhabit or predominate in the aquatic system. The most predominant cyanobacteria were Dolichospermum lemmermannii and Microcystis aeruginosa. Knowledge of the state of rivers, lakes and lagoons is of vital importance to avoid loss of biodiversity, reduction in the use of water resources and health problems such as intoxication in people who are in contact with toxic blooms.