The present study was undertaken in thirty cyanobacterial strains of Calothrix (family Rivulariaceae) to analyse their morpho-physiological and molecular relatedness. These strains including reference strain (UTEX 379) were procured from culture collection of Centre for Conservation and Utilisation of Blue Green Algae, IARI, New Delhi INDIA. Most of the forms were planktonic or free floating while some exhibited benthic growth behaviour. Variation in colour of thallus was expressed distinctly and the colour ranged from brown, blackish green to dark green. Large number of strains grew as floccose masses while some grew as spreading and few formed evenly distributed suspension. Microscopic examination revealed that the trichomes grew as densely entangled/distinctly or slightly constricted except in few where trichomes were irregularly straight or bent. The present analysis undertaken with different strains of Calothrix using morpho-physiological and molecular approaches, have clearly indicated a high degree of genetic diversity as well as relatedness.