Four mulberry genotypes with contrasting traits of water use efficiency and rooting were employed for this study. These genotypes were collected form the mulberry gene bank at Central Sericultural Research and Training Institute, Mysore, Karnataka, India. The Genomic DNA was extracted using HiPura Plant Genomic DNA Purification Spin Kit (HiMedia, India) and DNA stock was diluted to a uniform concentration of 10ng/?l for PCR amplification. ISSR-PCR amplification using new set of primers was standardized. Prior to genome amplification, annealing temperature of 15 ISSR primers were standardized. Other primers employed in the study were either did not find a complementary priming region or PCR conditions could not be optimized. The detail of standardization procedure followed is provided in Table 2. ISSR amplification by 15 primers generated a total of 148 markers of which 118 were polymorphic and thus accounting 79.72% polymorphism among the four genotypes studied. Ten mulberry specific SSR primers were also used for this study. These microsatellite primers were developed and designed by Department of Crop Physiology, UAS Bangalore. The SSR primers (F/R) could amplify a total of 17 microsatellite marker loci of which 11 (64.79%) were polymorphic (Table 3). Computation of the marker data from both ISSR and SSR amplification of parental lines using Dice dissimilarity coefficient resulted in a diagonal matrix. Maximum dissimilarity (0.4208) was recorded between Dudhia White and MS-3 and the least dissimilarity (0.2984) was recorded between U.P. and Dudhia White.