A great deal of research in the biogeography of marine and fresh water cyanobacteria has been carried out, but many unknown persist, and more work is needed to elucidate and understand thick complexity. The present investigation aimed at analyzing their distribution, generic diversity and abundance in selected ecologies such as river, ponds and rainfall of Melapponnanviduthy at Pudukkottai district. The physico – chemical analysis of water showed variations. Small pieces of microbial colonies of fresh water cyanobacterial isolates were picked out from the BG-11 medium for laboratory analysis. Totally ten genera were identified in the study. The selected cyanobacterial cultures were subjected to molecular characterization by using RAPD – PCR. Then the Phenogram generated revealed two clusters A and B. The cluster A was further divided into two sub clusters A1 and A2. The sub cluster A consist of two strains (Phormidium lucidum SG01 and P. lucidum SG02), and the cluster B having only one strain (Phormidium lucidum SG03). From the banding pattern, it was clearly shown that all the strains tested were different from each other.
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