Aim: Although many phylogeographic studies have focused on continental refugia, the roles of islands as refugia have long been overlooked. In this study, we conducted phylogeographic studies of a plant with insular distribution, Microtropis japonica, to elucidate the potential roles of islands as refugia during recent glacial periods. Specifically, we test the hypothesis that two remote groups of Japanese islands (the Izu and Ryukyu Islands) were refugia for M japonica. Location: The Izu and Ryukyu Islands of Japan and their adjacent areas including the Japanese mainland and Taiwan. Taxon: Microtropis japonica (Celastraceae). Methods: A total of 363 individuals were sampled from 44 populations of M japonica. To elucidate population genetic differentiation and demographic change in M japonica, we performed molecular variance and mismatch distribution analyses based on chloroplast DNA (cpDNA) sequence variations and Bayesian clustering and gene flow estimates based on nuclear single-nucleotide polymorphism (SNP) data. In addition, to examine distribution changes, ecological niche modelling using the maximum entropy method was used to determine suitable habitats existing currently or during the last glacial maximum, using occurrence data and six bioclimatic variables. Results: Both cpDNA and nuclear SNP data showed genetic differentiation between two disjunct regions. However, cpDNA data indicated genetic differentiation within the Ryukyu Islands but not within the Izu Islands, while nuclear SNP data indicated genetic differentiation within both island groups. Ecological niche modelling showed that both the Izu and Ryukyu archipelagos had contained some islands with a climate compatible with modern M japonica climate envelopes despite climate oscillations. Main conclusions: Islands within both the Izu and Ryukyu archipelagos may have supported M japonica populations throughout historical climate oscillations. The current disjunct distribution of M japonica strongly reflects its refugial locations during the last glacial period and the subsequent range expansion. Islands were important refuges, contributing to the modern disjunct distribution of M japonica.