DNA-based technology are about to revolutionize the analysis of population structures as well as the determination of individual indentities. Furthermore, the analysis of polymorphic DNA regions make it possible to reach detailed conclusions on family relationships of individual. Microsatellite loci are increasingly used in population genetic and evolutionary studies. Simple sequence repeats (SSRs) or microsatellites consisted of short tandem repeats (usually 1-6 nucleotide) have shown advantages over other markers. We report here the isolation and characterization of nine highly polymerphic microsatellite loci for phylogenetic and population genetic use in silkworm. Comparative analysis of diverse silkworm strains with microsatellite locus revealed several alleles and discriminative heterozygosity values. A list of primer sequences that tag each locus is provided. The usefulness of microsatellite markers can be expected to enhance the classification in silkworm.