Compared to tree species, there still remains a very limited number of phylogeographical studies on temperate forest perennials. In the present study, we used nuclear microsatellite markers to detect extant patterns of population genetic structure of the perennial plant Veratrum album ssp. oxysepalum in the understory of temperate forests, aiming to provide insights into the post-glacial history of the species and the reasons for the disjunct distribution of chloroplast DNA (cpDNA) haplotypes found in a previous study. We examined eight polymorphic nuclear microsatellite loci to examine genetic variation within and among 32 populations of V. album ssp. oxysepalum and seven populations of Veratrum stamineum. The population of V. album ssp. oxysepalum was split into two groups: those in the northern part of the Japanese Archipelago and all others. In addition, each population group was split into two subgroups. Only one population of V. stamineum included a substantial number of individuals categorized as V. album ssp. oxysepalum. The population genetic structure revealed by nuclear microsatellites suggests that V. album ssp. oxysepalum migrated from Eurasia into the Japanese Archipelago at least twice before the last glacial era through two different land bridges: the Korean Peninsula and Sakhalin. In addition, there appeared to be at least two refugia of V. album ssp. oxysepalum in each of the areas, dominated by the two different lineages from Eurasia during the last glacial era. The disjunct geographical pattern found in cpDNA variation in a previous study was blurred in the genetic structure as revealed by microsatellite markers, probably as a result of extensive gene flow via pollen. Currently, one-directional introgressive hybridization occurs from V. album ssp. oxysepalum to V. stamineum at only one locality; there is no evidence of the opposite pattern.