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Cyanobacteria play an important ecological role in every ecosystem with hidden economic and social impact. Among tropical countries, Sri Lanka holds a rich biodiversity with remarkable cyanobacterial diversity. The major objective of this study was to investigate the diversity of culturable cyanobacteria from freshwater bodies of Sri Lanka, with a phylogenetic perspective. Molecular characterization followed by phylogenetic evaluations allowed identification of new species with value added potential and revealed deeper taxonomic resolutions. A total of 74 monocultures were obtained. Rare isolates; Alkalinema pantanalense (U4), Geitlerinema sp.(U36) and Westiellopsis prolifica (U58) were also among them. Novel species Cephalothrix komarekiana was identified for the first time in Sri Lanka. This species was first reported from South American continent (Brazil and Amazonian rivers in 2015 and 2017 respectively) and Korea in 2018. The present study is next in line reporting the species first time from the tropical Asia. Higher value added potential and easy culturing of C. komarekiana suggest its economical applicability in many industries. Overall, this study provides insight on diversity, ecological distribution and industrial applicability of culturable cyanobacteria from the tropics with special reference to C. komarekiana reported from Sri Lanka.