Cyanobacteria are photolithoautotrophic organisms inhabiting different ecosystems all over the world thanks to their exceptional adaptability. Classification and taxonomy of cyanobacteria were at first based solely on their morphology and have changed significantly with the introduction of molecular methods and phylogenetic analyses. Polyphasic characterization is considered the best approach because it includes the analysis of several parameters, like phylogenetic, morphological, physiological and ecological traits of cyanobacteria. The aim of this study was to isolate and describe benthic taxons of cyanobacteria from epilithic habitats of supralittoral and mediolittoral zones of the eastern Adriatic Sea and epibiotic taxons of cyanobacteria from the carapace of loggerhead sea turtles, using polyphasic approach. A total of 34 laboratory cultures were isolated and classified into 4 basic morphotypes based on their morphology. Based on morphological and phylogenetic analyses that included 16S rDNA, 28 strains isolated from benthic habitats were classified into the genera Sodalinema, Salileptolyngbya and Nunduva, and were recorded for the first time in the Adriatic Sea. All 6 epibiotic strains isolated from the carapace of loggerhead sea turtles were classified in the genus Leptothoe, previously discovered on the carapace of sea turtles using metagenomics, and in this study were isolated into laboratory cultures for the first time. For future research a complete and accurate characterization of strains, including additional genetic markers in the phylogenetic analysis, is recommended to resolve the doubts in identification and classification and attribute to the description of taxons new to science.