In the present study, the morphology and genetic diversity of ten (10) potential cyanobacterial strains isolated from fresh water habitats of Loktak Lake was investigated by Restriction Fragment Length Polymorphism of 16S rRNA genes using four different enzymes viz., HinfI, AluI, EcoRI and TaqI. These enzymes digested the 16S rRNA PCR products and yielded different profiles. These strains showed high phycobili proteins content, extracellular ammonium excretion and nitrogenase activity when preliminary screening was conducted. The strains Nostoc spp. (BTA-60, 61), Nostoc commune (BTA-67) and Nostocmuscorum(BTA-950) were similar and delineated from the rest by the enzymes EcoRI and AluI. Other digests which characterized Calothrix sp. BTA-73 as a distinct taxonomic group from the rest was catalyzed by the enzymes EcoRI and AluI. On the basis of the genetic polymorphism band, HinfI, TaqI and AluI were also able to discriminate Anabaena sp. (BTA-964)from the other cyanobacterial strains. Phormidium spp. (BTA-52, 75, 1048) was similar and different from the rest of other strains as indicated by the enzymes EcoRI, TaqI and AluI. Within Nostocspp. group, there was no definite clustering for the morphological speciation of N. commune (BTA-67), N. muscorum (BTA-950) and other Nostoc spp. (BTA-60, 61, 80). Two Nostocstrains (BTA-61 and 67) with exactly the same profiles by digested banding pattern in EcoRIandHinfIwere confirmed as belonging to the same species. Non-heterocystous, filamentous Phormidiumout grouped from the heterocystous cluster but were still closely related to them and to each other. The clusters for four different enzymes yielded heterogenous groupings of the morphotypes and resulted in unclear delineation of the studied cyanobacterial strains.