Many critically endangered species require not only in situ but also ex situ conservation to reduce extinction risk. In this study, all five known wild populations and two artificially managed ex situ populations outside the species' native range of Polemonium kiushianum, a critically endangered herb species in Japan, were studied, using 10 polymorphic microsatellite markers to assess the genetic consequences of habitat degradation on the wild populations and the establishment of ex situ populations. Levels of genetic diversity among the wild populations were similar to each other, whereas genetic diversity in the ex situ populations was considerably lower than that of the wild populations. A significant level of genetic differentiation was associated with a recent bottleneck and genetic drift in the wild populations. The STRUCTURE analysis revealed that the genetic composition of the two ex situ populations differed from that of the five wild populations. The low genetic diversity observed in the ex situ populations and different genetic composition between wild and ex situ populations may be due to genetic drift with few founders for the ex situ populations and the management strategy used for the ex situ populations. Seed transfer simulations using simulated genotypes generated on computer programs indicated that 1000 or more seeds were needed to enhance genetic diversity and recover the genetic composition of the present ex situ populations. These simulations used to predict the genetic consequences of immigration represent a powerful tool for conservation management of critically endangered species based on genetic data. (C) 2012 Elsevier Ltd. All rights reserved.