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Molecular characterization of twelve varieties of Sorghum bicolor L. was carried out with 11 RAPD and three ISSR primers. Outof the different anchored primer combinations, ISSR primers with TC and GA motifs produced clear and maximum scorablebands, thus revealing a better coverage of the genome. Genetic diversity parameters [viz., average and effective number ofalleles, polymorphic information content (PIC)] were calculated for both RAPD and ISSR markers. UPGMA clustering based onJaccard’s coefficient was calculated. RAPD markers were more efficient than ISSR markers with regards to detection ofpolymorphism, number of bands scored and PIC values. Genetic variations detected among the geographically differentpopulations of Sorghum bicolor L. could be of much use for the introgression of new characters from wild counterparts to thecultivars, isolation of stable segregating markers and selection of improved varieties and conservation of germplasm resources.