Species range shift is thought to be associated with indigenous vegetation. Schizocodon soldanelloides is an herb that inhabits a wide altitudinal range; both alpine zones and the understorey of temperate deciduous forests in Japan. We aimed to elucidate the species’ range shifts to test whether this plant had a synchronous history with alpine plants and/or deciduous trees, or a distinct range shift history. Thirty-one cpDNA haplotypes from 38 populations showed geographic units of north-eastern, central and south-western Japan. Ecological niche modelling predicted a distribution during the LGM in the central mountainous region as a large area, but recognised the existence of refugia in north-eastern and south-western Japan. Centre populations would have persisted for long periods owing to less population bottlenecking and genetic drift. The high mountains of central Japan acted as refugia for the herb during coldest period. Current north-eastern and south-western populations were formed by subsequent range expansion from microrefugia during the postglacial period. The population dynamics of S. soldanelloides was inconsistent with that of other plants representative of its ecological niche. Climate oscillations had differential effects on each plant species’ range shift, despite their current co-distribution.