In order to understand the diversity and genetic relationships of silkworm strains preserved in Korea, we genotyped 78 Bombyx mori strains (Bombycidae: Lepidoptera) originating from Japan, using eight polymorphic microsatellite loci. We obtained per-locus allele numbers ranging from 5 to 16 (with an average value of 9.1), per-locus observed heterozygosity ranging from 0.13 to 1.00, and per-locus polymorphic information content ranging from 0.36 to 0.77, indicating that some loci are highly variable. Phylogenetic analysis with the eight concatenated microsatellite loci showed no clustering based on known strain characteristics and origin. Nineteen strain-specific apomorphic alleles, which discriminated 16 of the 78 silkworm strains, were obtained from eight loci. These strain-specific alleles can thus be utilized for routine discrimination of strains from Japan, without any further typing of other loci. Homozygotes were also observed at some loci (27 of 118 genotypes), which can also be used to discriminate several strains by typing a few loci. These results showed that eight microsatellite loci described herein were sufficiently variable to discriminate among the 78 silkworm strains we examined, and may be useful for future investigations of this economically important species.