During the last two decades benthic Cyanobacteria have become more prevalent on coral reefs sites around the world, covering sand, silt, rocks and algae. The abundance of these mats has been associated with widespread signs of reef degradation. On particular sites the cyanobac-terial abundance is remarkably higher than on others. There are no present studies comparing the differences and similarities of cyanobacterial mats between those particular sites. The aim of this study was to characterize and compare the diversity of benthic Cyanobacteria from sites with low cyanobacterial abundance and sites with a high abundance of cyanobacterial mats. To ensure the reliability of the identification results a polyphasic approach was used that combines phenotypic and phylogenetic analyses. For the genetic characterization partial 16S rRNA gene sequences were compared with an existing online databank. Morphological iden-tification was performed using light microscopy. The genetic and morphological characteriza-tion corresponded to 60 percent. That is an acceptable result considering that no axenic cul-tures were used. All benthic cyanobacterial mats consisted of species from the filamentous genera Oscillatoria, Lyngbya, Phormidium, Symploca, Dichothrix or Trichocoleus. Crucial differences of benthic cyanobacterial mat composition could be detected between sites with low cyanobacterial coverage and sites with a high abundance of cyanobacterial mats. The diversity of benthic cyanobacterial species at sites with low benthic cyanobacterial coverage was respectively higher than on sites with high abundance of cyanobacterial mats. Further-more the species Hydrocoleum glutinosum and Lyngbya majuscula were characterized to be mainly responsible for the extensive mats at sites with high coverage rates.