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Digestive amylase has been identified as a useful marker for breeding in the silkwrom, Bombyx mori L (Lepidoptera: Bombycidae), due to its wide genetic divergence, its role in better digestibility and robustness. The low yielding indigenous B. mori breeds of tropics like India are characterized by high activity amylase genes controlled by Amy div or dv alleles, while the high yielding breeds of temperate origin are endowed with ‘null’ type (Amy dn) with low activity. For improving the digestibility and survival of temperate breeds of Japanese origin, Near Isogenic Lines (NILs) were developed introgressing the Amy div and dv alleles from the Donor Parents (DPs) into the genetic background of the Recurrent Parents (RPs) with ‘null’ type of amylase, which showed significant improvement in viability of the NILs. With the objective to know whether the amylase gene itself may confer higher survival by improving digestibility or some other closely linked genes flanking the amylase locus is responsible for better viability of the NILs, RAPD profiles among six B. mori breeds comprising of the DPs, RPs, and NILs developed through introgression of Amy div or dv alleles were analysed using 27 sets of RAPD primers. Out of the 27 primers, six (OPA01, OPA06, OPA09, OPA15, OPAH03, and OPAH05) showed RAPD products linked to the amylase genes of the DPs introgressed in the NILs, which were absent in their respective RPs. Three amplicons of 1584 bp, 1904 bp, and 1232 bp were specific to Amy div allele and one amplified product of 1776 bp was found to be linked with the Amy dv allele. Interestingly, two PCR products of 2628 and 1375 bp were associated with both Amy div and dv alleles. The results are discussed in light of further characterization of these amplified products leading to identification of DNA sequences that may be responsible for better digestibility and higher survival in B. mori.