In Morocco, poisoning events of fish, aquatic birds and livestock have been observed in some reservoirs and shallow lakes. In all cases, the reasons for animal mortality reasons have not been confirmed and the toxic cyanobacteria strains that were abundant in these water bodies have been suggested as their cause. Since 1994, the authors started taxonomic, ecological and toxicological studies by collecting samples from various lakes reservoirs and ponds. The results show that more than 18 out of 26 lakes reservoirs used for human water supply contained at least one species of planktonic cyanobacteria, where the genus Microcystis was dominant (Microcystis aeruginosa f. aeruginosa, M. aeruginosa f. flos-aquae, M. ichthyoblabe, M. pulverea f. delicatissima) and was associated with Oscillatoria, Planktothrix, Anabaena, Aphanizomenon, Phormidium and other genera. Taxonomic studies shows that among more than 150 cyanobacteria taxa identified in Moroccan freshwater ecosystems, 35 are potentially toxic. For several species, the toxicity of both natural blooms and isolated strains lyophilized material was confirmed by mouse bioassay and the microcystins content evaluated by the Enzyme-linked immunosorbent assay (ELISA). A map of geographic distribution of Microcystis strains inventoried in moroccan water bodies is presented.