Cettia diphone diphone is a subspecies of the Japanese Bush-warbler that is endemic to the Bonin and Volcano Islands of the Ogasawara Islands. Although the two island groups are physically distant and have different geological histories, genetic and morphological relationships between the two populations are unknown. A few individuals of an unidentified subspecies have been observed since 2007 on Mukojima of the Bonin Islands. They were possibly wintering birds of another subspecies in light of their song pattern and appearance. We examined the genetic and morphological differences among the Bonin and Volcano populations of C. d. diphone, C. d. cantans, and C. d. sakhalinensis populations and determined the identity of the unidentified subspecies on Mukojima by comparing sequences of the CO1 region of the mitochondrial DNA (mtDNA) and conducting a canonical discriminant analysis (CDA) using five measurements per bird. Our results indicate that these populations (except C. d. sakhalinensis) are genetically and morphologically different. They did not share any haplotypes of mtDNA and indicated high discrimination rates (over 75%) based on CDA. Because the Volcano population inhabits only one island, it is a priority for conservation. The unidentified individuals on Mukojima Island are not the native subspecies. Migratory individuals might colonize Mukojima due to improved habitat conditions and an available niche. Continuous monitoring of the Mukojima population and its impact on native C. d. diphone is required.