Abstract: Fusarium wilt, caused by the soil-borne fungus Fusarium oxysporum f. sp. cumini, can lead to significant yield losses in cumin (Cuminum cyminum L.) locally known as Zeera. Ten F. oxysporum isolates from cumin plant were obtained from diseased plants of different cultivated areas of Rajasthan and characterized for pathogenicity and Vegetative Compatibility Grouping (VCG). The isolates were placed into six VCG groups based on pairing of complementary mutants. To find out correlation between genetic diversity and pathogenecity RAPD analysis was carried out using 40 UBC (University of British Columbia, Vancouver, Canada) primers, generated 41 polymorphic markers out of 65 amplicons with 63.07% average polymorphism. Based on Ntsys analysis of RAPD data was clustered all the genotypes in two major groups (group A and B) at 66.25% between group similarities. The results suggest that phylogenetic relationships among fungal isolates, collected from different regions of Rajasthan correlates with variation exist at pathogenicity.