Whether the temperate forests of Japan were confined to coastal regions during the Last Glacial Maximum as evidenced by pollen or persisted in additional refugia within inland regions has not been adequately resolved. This study investigates the phylogeography of a temperate conifer Sciadopitys verticillata (Sciadopityaceae) combined with LGM paleodistribution modelling to test whether the species conforms to the pollen-based coastal refugia model or was able to survive outside these areas. A total of 2,213 bp of chloroplast DNA and 405 bp of mitochondrial DNA were sequenced for 354 samples from 31 populations across the species range. Chloroplast DNA showed significant geographical structure with the highest diversity and differentiation in the northern part of the species range in inland central Japan, while southern populations were dominated by a widespread haplotype. In contrast, the mitochondria had no obvious geographic structuring. Paleodistribution modelling provided independent support for a central Japan glacial refugium. This study provides compelling evidence for the persistence of S. verticillata outside the major pollen-based LGM coastal refugia, most likely within inland river valleys. Further research is required to better understand the range limits of temperate species during glacial periods in Japan.