Artificial selection has been widely utilized in breeding programmes concerning the commercially important silk-producing insect Bombyx mori. Selection increases the frequency of homozygotes and makes homozygous effects stronger. Molecular variation induced by selection in the inbred population of B. mori strain Nistari, was assessed in terms of genic differentiation by using a polymorphic profile generated by RAPD and ISSR marker systems. Artificial selection for longer larval duration (LLD) for 4 generations resulted in a significant prolongation of larval duration (F = 89.28; P = 5.14?10?7). The lines selected for shorter larval duration (SLD) were not significantly different from the control group. RAPD and ISSR primers generated polymorphic profiles when amplified with genomic DNA of individuals of LLD and SLD lines. Distinct markers specific to LLD individuals were observed from the 3rd generation and indicated selection-induced differentiation of allelic variants for longer larval duration. Both SLD and LLD were characterized by high gene diversity (h 0.197) and total heterozygosity (Ht 0.26), low homogeneity (?2 test, p < 0.005) as well as a large coefficient of gene differentiation (Gst 0.42) but low gene flow (Nm 0.42). Genetic distance was the highest (0.824) between 3rd generations of SLD and LLD. High heterozygosity and prolonged larval duration substituted for shorter larval duration (the traditional trait of fitness) in the Nistari LLD larvae.