Molecular variability of Puccinia sorghi pathogen was carried out in the laboratory of 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 suitable maize varieties against common rust disease which seriously affects maize productivity.Results revealed that, phylogenetic analysis grouped Puccinia sorghi, isolates into two main clusters with 0.030 similaritycoefficient. The similarity coefficient ranged from 0.001 to 0.034 indicating good level of similarity. UPGMA clusteranalysis based on genetic distance coefficients clearly separated the all isolates. Out of five isolates Gadag, Badami andNippani isolates were grouped under cluster I, where as Dharwad and Hirekerur isolates formed separate cluster II. Incluster I, Gadag and Badami isolates were showed almost zero per cent of divergence, compared to Nippani isolate whichshowed 0.8 to 0 .9 per cent of divergence. Wherein, cluster II Dharwad and Hirekerur isolates were present with nearly 3.34per cent divergence compared to cluster I. This indicated there was 96.66 per cent of similarity among the isolates ofPuccinia sorghi.