The marine benthic cyanobacteria on coral reefs of Moorea Island (French Polynesia) show significant changes in species diversity in response to environmental impacts. To study these changes in cyanobacterial diversity, we examined pristine and degraded coral reefs by combining microscopy of morphological properties of the taxa with characterization of each by 16S rRNA gene sequences. A total of 30 cyanobacterial species have been recorded, of which 10 (33%) of them represent a new record for Moorea Island. The majority of morpho-species we identified could be distinguished by phylogenetic analyses of 61 sequences. Our survey results showed a sharp distinction in the composition of benthic cyanobacterial assemblages from healthy (high living coral cover) versus degraded habitats (low live coral cover due to anthropogenic activities). Finally, 21 bloom-forming species were identified, occurring mostly in environmentally impacted area (north coast). Blooms were dominated by three species: Anabaena sp.1, Hydrocoleum majus-B, Lyngbya majuscula. This study provides novel insights into the taxonomy of tropical benthic cyanobacteria as important environmental indicators and advocates the use of new bioevaluative tools for the management of coral reef environments.