Recently in Japan, approximately six million quails were primarily being reared for commercial egg production. It is believed that almost all commercial quails in the country became extinct during World War II, and that the present commercial gene pool was restored from the limited number of surviving birds. The present study evaluates the genetic diversity within and differentiation between 12 laying-type Japanese quail lines on the basis of 45 microsatellite genotypes. The mean number of alleles per locus and the expected heterozygosity within a quail line were 5.22–5.69 and 0.601–0.618, respectively. These results showed that laying-type quail lines in the present study exhibited a higher degree of genetic diversity than experimental quail lines in a previous study. Pairwise genetic differentiations (F_ST) between lines were significant but weak (F_ST=0.0028–0.0254; 57.6%), and no significant differentiations were found between the remainder. This was also confirmed by genetic clustering analyses, in which individuals did not form independent clusters consistent with their line origins. The results of the present study indicate relatively high genetic diversity within and no clear genetic differentiation between laying-type quail lines. Absence of genetic differentiation may reflect the breeding history of laying-type quails.