RFLP clones harbouring multi-copy DNA sequences were isolated from the Pst I sub-genomic library of the indigenous silkworm race, Nistari, and were used for DNA fingerprinting studies in 13 stocks of silkworm, Bombyx mori L. Six multilocus probes produced 180 RFLP markers that showed a high level (98%) of polymorphism and are highly useful in molecular mapping, genotype characterization and marker assisted selection (MAS). The dendrogram derived from UPGMA analysis clearly divides the 13 silkworm stocks into two major clusters: high- and low-yield stocks. Furthermore, adopting multiple regression analyses, the RFLP marker(s) associated with characters of economic importance were identified, a first of its kind for any species of insect of commercial importance. The results obtained create an opportunity of using germplasm stocks directly for isolating specific RFLP band(s) and use it for MAS in breeding programs.