This dataset contains the species occurrence record of zooxanthellate reef‐building corals at 1059 sites on the Japanese coast, recorded from 1929 to 2020. We compiled coral occurrence data including 482 species from 162 literature sources, most of which were written in Japanese and published as gray literature in local journals or individual reports. This dataset is published as a data paper in Ecological Research (see https://doi.org/10.1111/1440-1703.12136).