In Morocco reservoirs and shallow lakes poisoning events of fish, aquatic birds and livestock have been observed during Summer. In all cases, the mortality reasons have not been confirmed, the toxic cyanobacteria strains that were abundant in these water bodies has been suspected. In order to establish a screening of potential toxic cyanobacterial strains in Morocco, the authors started taxonomic and ecological studies since 1994 by collecting samples from various lake reservoirs and ponds. The results show that 14 out of 26 lakes reservoirs used for human water supply contained at least one species of planktonic cyanobacteria, where the genus Microcystis was dominant (M . aeruginosa f. aeruginosa; M. aeruginosa f. flos-aquae; M. ichtyoblabe; M. pulverea f. delicatissima ) and associated with Planktothrix, Anabeana, or Phormidium species. Among of 150 cyanobacterium taxa identified from Moroccan freshwater ecosystems, 34 species are potentially toxic. In particular conditions, as in brackish Oued Mellah reservoir, the blooms of Microcystis ichtyoblabe was substituted by those of Aphanizomenon flos-aquae associated with Planktothrix. By using electronic microscopy, a comparison of cytology between the most frequent cyanobacetrium (M. aeruginosa f. aeruginosa and M. ichthyoblabe ) cells has been performed. In term of this study, a map of geographic distribution of all potentially toxic cyanobacteria species identified from Moroccan water bodies will be presented and discussed.