Aim Although the evolution of island endemic plants has long been investigated, the majority of such studies have focused on species with remarkable levels of morphological variation and on islands substantially far from the mainland. Endemic plants on nearshore oceanic islands have received less attention. We investigate the population genetic structure and dynamics in plants endemic to nearshore and recently formed oceanic islands and examined the possibility of multiple colonizations onto the islands. Location Japanese mainland Honshu and the adjacent Izu Islands. Taxon Solidago virgaurea (Asteraceae). Methods Sixteen and nine populations of S. virgaurea complex were sampled from the mainland and islands respectively; phylogeographical and population genetics analyses, including Bayesian Phylogeographic and Ecological Clustering (BPEC) analysis and Discrete Phylogeographic Approach (DPA) to trace the history of colonization events onto the islands, were performed using plastid DNA and nuclear microsatellite DNA variations. Results Phylogenetically close plastid DNA haplotypes were shared between the mainland and islands, although the populations of S. virgaurea from different islands tended to exhibit phylogenetically distinct haplotypes. Admixture analyses based on nuclear DNA variations revealed distinct genetic structures between the mainland and island populations. Gene flow among islands is restricted but may partially offset genetic drift on each island. Main conclusions The genetic structure observed in this study may not have originated from a single dispersal event and successive expansion but rather from at least three colonization events and subsequent gene flow among island populations. Based on the nuclear DNA variations, the Izu Island populations of S. virgaurea are genetically distinct from the mainland ones. Repeated colonization events may have provided sufficient genetic diversity, which would generally be susceptible to founder effects and exert a driving force for evolutionary adaptation, to these oceanic island populations.