Molecular variability of Ramularia areola pathogen was carried out in the laboratory, Department of PlantPathology, College of Agriculture Dharwad, University of Agricultural Sciences, Dharwad by molecular methods using ITSprimers and subsequently subjected to sequence analysis during 2015. Molecular variability in the pathogen served as aguideline for breeding the suitable cotton varieties against grey mildew disease of cotton which severely affects cottonproductivity. Results revealed that, Phylogenetic analysis grouped Ramularia areola isolates into two main clusters with0.12 similarity coefficient. The similarity coefficient ranged from 0.001 to 0.12 indicating good level of similarity. UPGMAcluster analysis based on genetic distance coefficients clearly separated the all isolates. Out of four isolates, Dharwad,Arabhavi and Naragund isolates were grouped under cluster A, where as Devihosur isolate formed separate cluster B. Incluster A, Dharwad and Naragund isolates were showed only 3 per cent of divergence, compared to Arabhavi isolate whichshowed 5.8 per cent divergence. In cluster B only one isolate Devihosur was present with nearly 12 per cent divergencewith cluster A. This indicated there was 92.00 per cent of similarity among the isolates of Ramularia areola.