Groundnut (Arachis hypogaea L.) is an oilseed crop largely grown throughout the world. Ten isolates of S. rolfsii collected from groundnut grown areas were investigated for their morphological and genetic variability study. Morphological variability among the isolates was confirmed based on sclerotia distribution pattern, colours of sclerotia, number of sclerotia produced by isolate, weight of hundred sclerotia and different diameter sizes of sclerotia. Genetic diversity among the isolates was confirmed by using ITS primers that produced rDNA amplicon size ranging from 650-700bp which confirmed that all isolates belong to Sclerotium. RAPD primers confirmed genetic variation among the isolates. Highest numbers of amplicons (13) were observed in the OPA-9 primer. 105 polymorphic and monomorphic bands were produced by RAPD primers. Isolates SrA-SrH (0.575), SrBKN-SrA (0.384) and SrBKN-SrBKL (0.330) exhibited highest similarity coefficient. Based on dendrogram generated by UPGMA, SrBKN, SrA, SrH, SrJPF, SrJPP and SrT isolates were considered in Groups I. SrBKL shows highest (51%) diversity in Group II while Churu (SrC) isolate showed 49% diversity in Group III. Dendrogram and cluster analysis cleared that Group I was more genetically diverse among the isolates. Morphological and molecular diagnosis of the pathogen has a pivotal role in the implementation of chemical (fungicide) and biological (bio-agents) methods. Morphological study and diagnosis of pathogen by ITS and RAPD primers further exploited for genetically diverse strains of S.rolfsii.