The Bonin (Ogasawara) Islands are subtropical oceanic islands in the northwestern Pacific. Reflecting their ancient origins, previous studies on plants of the Bonin Islands reported evolutionary phenomena that are common to oceanic islands, such as high endemism and accelerated diversification. In this article, we demonstrate the first example of loss of seed dispersibility during the evolutionary processes of the plants of the Bonin Islands. Seed buoyancy and morphology of Hibiscus glaber, a tree endemic to the Bonin Islands, and H. tiliaceus, a pantropic species, were examined. The latter is the progenitor species of H. glaber. Average ratios of floating seeds per tree were 0.2 and 0.8 for H. glaber and H. tiliaceus, respectively, in a 3% NaCl solution. There was considerable variation among individual H. glaber trees, ranging from 0 to 0.89. The air space inside the seed coat was generally smaller in H. glaber than in H. tiliaceus. Loss of seed buoyancy in H. glaber is due to decreased air space in the seeds. It is plausible that loss of seed buoyancy occurred in response to the habitat shift inland during the speciation process of H. glaber from the coastal species H. tiliaceus.