Ecosystem in the Bonin Islands is highly vulnerable to the invasion of alien species, and administrative organs have been carrying out the extermination of invasive alien species. After the removal of alien species, transplantation of native plants is considered to be effective for restoration of the fragile ecosystem. Plant populations in oceanic islands might be genetically differentiated within and among islands. Therefore, transplantation among populations might disturb the historical genetic structure of the species. In order to prevent artificial genetic disturbance by transplantation, we have to understand genetic structure of candidate species prior to transplantation. In this study, we estimated genetic diversity and population genetic structure of Ochrosia nakaiana (Apocynaceae) using microsatellite markers. Ochrosia nakaiana is endemic to the Bonin Islands, common dominant species in the mesic and dry forest of Chichi-jima and Haha-jima Islands. We performed genetic analyses for 458 individuals of O. nakaiana from 16 populations on 7 islands of the Bonin Islands. We discuss the planting guideline of O. nakaiana for proper management based on genetic diversity and differentiation between populations.