We developed simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) of Sciadopitys verticillata (Sciadopityaceae) which is an endemic Japanese evergreen conifer species. Eleven loci were chosen which showed clear polymorphic patterns from three populations, with 2–9 alleles per locus. Two loci showed significant deviation from Hardy–Weinberg equilibrium in at least one population. No significant genotypic disequilibrium was detected for any pair of loci after the significance levels were adjusted by Bonferonni-type procedures.