Abstract: Most of the marine cyanobacteria especially to the order Chroococcales, Oscillatoriales, Nostocales occur ordinarily as planktonic forms. Their taxonomic assignment was based on morphological and cytological characteristics. The genetic variation in the species and strain level morphological and cytological features is not reliable and molecular characterization of cyanobacteria is necessary for better identification. The samples were collected from Thondi and Kattumavadi in Palk Bay region of Tamil Nadu, India. Biodiversity of cyanobacteria were documented, purified and maintained. The two strains, Phormidium chlorinum NTMP01 and Jaaginema psedogeminatum NTMP02 were selected for further molecular characterization based on 16S rDNA sequence in the strain. Evolutionary relationship and secondary structure was constructed with the sequence. The sequences were submitted to GenBank with accession numbers GU812856 and GU812857.