The Oita salamander Hynobius dunni Tago, 1931, endemic to eastern Kyushu and western Shikoku of southwestern Japan, is a lowland lentic breeder and has declined throughout its distribution range. To contribute to the future conservation of this salamander, current population genetic structures and genetic diversities were examined for 12 populations of eastern Kyushu, using a mitochondrial cytochrome b gene and three microsatellite loci. Populations were found to be genetically separated into northern and southern groups, and microsatellite analysis showed some genetic differences even in the northern regions. The southern group was restricted to a narrow area and had low genetic diversity in both mitochondrial and microsatellite DNAs. In the northern group, the mitochondrial and microsatellite DNA diversities were also low in some peripheral populations. For the accurate genetic management of this species, we need to pay more detailed attention to such genetic differentiation and diversity.