Due to morphological convergence and the application of numerous taxonomic concepts, the systematics of filamentous cyanobacteria is still a significant problem. The incorporation and integration of modern molecular, cyto-morphological and ecological approaches in cyanobacterial taxonomy are essential and must be acknowledged as the valid methods for the development of their modern systematics. In this study, method of using 16S rRNA gene sequences to infer the genetic relationships of twelve freshwater cyanobacterial isolates amongst themselves was evaluated. The taxonomic resolution was inferred from their phylogenetic tree, in silico restriction digestion analysis and secondary structure prediction. These methods allowed cyanobacterial genera to be well distinguished with their genotypic and phenotypic differences. Amongst twelve strains, Spirulina subsalsa with highest protein content was used in this study for evaluating the stability of Curcumin which is a curcuminoid compound reported from Curcuma longa. Though they have wide properties, they still lack stability and bioavailability. It is reported previously that microbes are used for biotransformation and act as a carrier molecule. Therefore, in this study, Spirulina incorporated with curcumin resulted with pH stability of curcumin and were found to have a biotransformation into Calebin-A, curcuminoid compound originally present in smaller amount (0.005%) in C. longa with various biomedical applications.