Abstract: The most challenging hurdle facing Pakistan is the production of Brassica germplasm with a wider genetic base and using them properly in rapeseed genetic improvement. Genetic diversity was evaluated in 20 rapeseed lines (10 entries each of B. napus and B. campestris) using RAPD as molecular markers. Four Randomly Amplified Polymorphic DNA primers were used to estimate the genetic distances among the genotypes in all the possible combinations. The genetic diversity study revealed different levels of polymorphism for RAPD primers GLA07, GLB07, GLD18 and GLE07 that resulted in amplification of 3.2, 1.5, 3.0 and 3.5 scorable bands (loci) per genotype of Brassica napus and 2.5, 1.3, 2.6 and 3.7 scorable bands (loci) per genotype of B. campestris. Among Brassica napus genotypes, maximum genetic distance (79%) was observed between Torch+Maluka, Torch+Baro and Torch+Global, while, maximum genetic distance (91%) was observed between T-16 and P1-367601 genotypes of Brassica campestris. Individual genetic distance observed among the B. napus and B. campestris lines ranged from 21.50 to 59.41% and 53.75 to 60.09%, respectively. The dissimilarity coefficient matrix of these lines based on the data of four RAPD markers using UPGMA (Unweighted Pair Group of Arithmetic Means) method was also used to construct a dendrogram. The dendrogram analysis indicated that lines Torch and 366822 of B. napus, while 2163 and P1-392029 of B. campestris were genetically apart from other lines. These results provide valuable information for fingerprinting that can be used in a synergistic way to create wider genetic base and augment the breeding program of Brassica in Pakistan.