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Cyanobacteria are phototrophic gram negative prokaryotes which include more than 150 genera and 200 species. Tropical marine ecosystems harbor a specific cyanobacterial flora while those forming the benthic community are known for their profilic source of natural products as well as their toxin production. Since no recent research had been entertained in determining the diversity of benthic cyanobacteria in Mauritius, this study aimed at identifying the benthic mat-forming cyanobacteria which inhabit the Mauritian lagoons. Samples were collected around the coastal areas of the Island during the summer season from Blue Bay, Albion, Balaclava and Grand River South East. Based on phenotypic and genotypic characters, 11 cyanobacterial strains were successfully identified to genus level, out of 12 samples collected. DNA extraction was performed using a Chelex-100 method which resulted in amplifications products when PCR was carried out. These cyanobacteria belong to the filamentous group of Lyngbya, Leptolynbya, Oscillatoria and Anabaena genera and the non-filamentous group of Merismopedia genera. Phylogenetic inferences based on 16s rRNA sequences revealed that the cyanobacterial strains evolved from a common ancestor, forming monophyletic clades. The identification of cyanobacterial strains up to the species level was not successful using both morphological and molecular characterization, suggesting the need for other important information such as ultrastructural morphology, ecophysiological characters or whole genome sequencing to ascertain their identity.