Cyanobacteria are an extremely diverse group of prokaryotes that inhabit various ecosystems. They are one of the major microbial groups found in the paddy soil microbial community and provide a valuable contribution, to the soil fertility by fixing atmospheric nitrogen. Thus cyanobacteria are considered as potential bio fertilizers for paddy cultivation. In this study, nine cyanobacterial taxa from paddy soils (0-10 cm) of the Intermediate Zone of Sri Lanka were isolated and identified using culture based (BG 11 medium) morphological analysis. Both unicellular (Aphanothece, Chroococcus, Johannesbaptistia, Microcystis) and filamentous (Anabaena, Pseudanabaena, Nostoc, Stigonema, Trichodesmium) genera of cyanobacteria were identified. DNA extraction was done by modified Boom’s method, with pre-treatment. Cyanobacterial cultures were maintained at 24 C temperature and 2,000 lux light at 60 rpm. Abundance of two cyanobacterial genera (Chroococcus and Microcystis) were confirmed by molecular analysis using Polymarase Chain Reaction (PCR) with specific primers CYA359F and CYA781R (b) for unicellular cyanobacteria.