Distribution shifts and natural selection through past climatic changes are important factors in determining the genetic structure of forest species. Kimura et al. use a combination of phylogeography and species distribution modelling methods to identify the responses of Cryptomeria japonica, endemic to the Japanese Archipelago, to past climatic changes. They identify four gene pools, one of which is likely to have been established by cryptic refugia. An ambiguous genetic diversity cline along elevations would be predicted by the distribution pattern and accessibility of refugial populations after the last glacial maximum, suggesting multiple refugia and/or admixture events affected the overall structure of genetic diversity.