<p><span style="font-size:14px"><span style="font-family:Arial,Helvetica,sans-serif">Studies on various nitrogen fixing microalgal strains found in the rice paddy field soils are carried out in different parts of the world. In the present study two cyanobacterial strains belonging to the order nostocales, <em>Calothrix</em> sp. and <em>Microchaete</em> sp. were isolated from the rice fields of Karimganj district, South Assam, India and characterized based on their morphological, biochemical and molecular analysis. For the phenotypic characterization - growth, pigments (chlorophyll <em>a</em>, total carotenoid content, phycobiliproteins) and biochemical properties (total carbohydrate and soluble proteins) were studied. The study showed that both strains contain lower phycoerythrin content as compared to the other pigments. The <em>Microchaete</em> strain contain a higher total carotenoid content while chlorophyll <em>a </em>accumulation was higher in the <em>Calothrix</em> strain. Phylogenetic compairision was made using 16S rRNA gene sequences including other sequences of <em>Calothrix, Microchaete</em> and <em>Tolypothrix</em> species from GenBank. The results showed that polyphasic approach provides necessary information for the identification of cyanobacterial species using morphological analysis in combination with molecular techniques.</span></span></p>