Cyanobacteria blooms in freshwater often pose a threat to public health and the environment due to toxin production or taste and odour problems. Blooms can be caused by various genera of cyanobacteria and thus, characterization of the cyanobacterial community becomes critical. a mock community containing eight known species as well as complex environmental samples were studied in order to evaluate the taxonomy precision of three 16S rRNA gene variable regions (V1-3, V4-5, V6-8).