Veronicastrum villosulum is a critically endangered herb, with only three populations remaining in Japan, Turugi in Tokushima prefecture, Ikeda in Gifu prefecture and Isumi in Chiba prefecture. The objective of this study was to reveal the genetic diversity and structure of V. villosulum and to apply this knowledge to the future conservation management of the species.

A total 179 individuals of V. villosulum were collected and the genotypes were determined using nine nuclear microsatellite markers developed for this study. The numbers of samples were as follows: 139 individuals from the Turugi wild population, 38 individuals from the Ikeda population and two individuals from the Isumi wild population.

Microsatellite analysis of all 179 individuals revealed three multilocus genotypes. We found that the Turugi wild population of V. villosulum was composed entirely of one clone (genet A). The Ikeda population was also one unique clone (genet B). The genotype of the Isumi population showed unique alleles at the eight loci, while one locus failed to amplify. Overall, this research shows that the Turugi, the Ikeda and the Isumi populations are distinct lineages and all of three must be given equal priority for conservation management.