Okinotorishima Island is an isolated table reef in the southernmost territory of Japan. To promote research activities on Okinotorishima, it is essential to collect, organize, and disseminate the scientific information that has been accumulated to date. This dataset is based on the "Database of Okinotorishima and Minamitorishima—Reference Section" (https://umdb.um.u-tokyo.ac.jp/DChiri/okinotorishima_minamitorishima/index.php), which was developed by the Okinotorishima and Small Island Program of the University of Tokyo Ocean Alliance with funding from the Tokyo Metropolitan Government. The dataset compiles biological occurrence records extracted from the literature and structures them in Darwin Core format.