Inter simple sequence repeats (ISSR) and random amplified DNA polymorphism (RAPD) markers were used to estimate the genetic diversity among 14 tropical silkworm races (Bombyx mori L.) for identifying potential parents to be used for hybrid preparation for commercial exploitation. High polymorphism (70.91 and 74.70%) was revealed by ISSR and RAPD markers. The dendrograms generated, using unweighted pair group method using arithmetic average from these markers, grouped the 14 silkworm races into two major groups, which corroborates the differences in cocoon characteristics. Discriminant function analysis of ISSR and RAPD markers identified three functions for cocoon weight and two functions for shell weights, respectively. Step-wise multiple regression analysis identified six ISSR markers (834500, 8841700, 8841850, 8271500, 8401500 and 7891250) and seven RAPD markers (834500, 885900, 8101400, 884900, 8361500, 7891250 and 7621700) significantly associated with cocoon and shell weights. The genetically divergent parents, identified through this study, can be used for the preparation of hybrids for commercial utilization. Similarly, the DNA markers identified can be utilized for marker-assisted selection along with those identified through quantitative trait locus mapping by others. Thus the information generated in this study is useful in silkworm breeding programmes in the tropical sericulture industry.