Bryan's Shearwater (Puffinus bryani) was described in 2011 on the basis of a specimen collected on the Midway Atoll in 1963. This specimen and another recorded on Midway in the early 1990s are the sole reliable records to date. Since 1997, we have found six specimens of a remarkably small Puffinus shearwater morphologically similar to Bryan's Shearwater on the Bonin Islands, northwestern Pacific. In this study, we examined the Bonin samples genetically and confirm that they are of Bryan's Shearwater. A morphological analysis suggests that the small body size and relatively long tail are characteristics of this species. Because the most recent individual was found on an islet to the north of Chichijima Island in 2011, the species has evidently survived in the Bonin Islands, where it may breed, although the exact location remains unclear. Three of the individuals found on an islet off Chichijima Island were carcasses preyed upon by black rats (Rattus rattus). Attempts were made to eradicate rats from this island in 2008, and rats may pose a problem on other islands where the shearwaters may breed. Regardless, Bryan's Shearwater appears to be very rare and threatened on the Bonin Islands. To conserve this species effectively, its breeding sites must be identified and the infesting rats eradicated.