A population genetic analyses was conducted on 250 moths of A. assamensis representing seventeen populations collected from North-east India using a ISSR-PCR strategy developed in our lab with mononucleotide anchored primers based on repetitive sequences from lepidopteran genomes. High genetic diversity was observed among and within the collected populations of this economically and culturally significant sericigenous moth, disputing the popular notion that these insects are genetically uniform and intractable for insect improvement or breeding programs. Cloning, sequencing and sequence analyses of polymorphic loci suggest that mobile elements and repetitive sequences play a major role on contributing to the genetic diversity found among individuals of seventeen populations of A. assama collected from silk farmers, government rearing depots and the forests of North-east India. Our results have possible ramifications on (1) development of breeding programs to improve silk production and reduce collections of “wild” cocoons from the forests; (2) endorsement of public policy for the need to conserve genetically distinct wild populations and identify safe corridors.