We investigated the genetic structure of Sciadopitys verticillata, an endemic conifer in Japan, using 11 microsatellite markers. Average expected heterozygosity varied from 0.282 to 0.450, with between 2 and 17 alleles per locus, and allelic richness varied from 2.14 to 2.94 within a population. Wilcoxon signed-rank tests suggested that there was a recent bottleneck in the southwestern populations in the Kinki district and in isolated northeastern populations in the Tohoku district. Bayesian clustering analysis showed that the populations of the Chubu, Kinki, and Shikoku districts were admixed from several clusters. Archaeological data suggest past anthropogenic exploitation for building and coffin material.