We describe a new species of lentic salamander of the genus Hynobius. From our examination of specimens from the Kyushu and Shikoku populations of Hynobius dunni, individuals of each population have distinct morphological and molecular traits. On this basis, we describe the Shikoku population as a new species. Morphological comparisons revealed that most individuals of H. dunni possessed distinct black spots on the dorsum, but that the new species lacks these spots. Furthermore, the mean snout–vent length was smaller for the new species than for the Kyushu population of H. dunni. Phylogenetic analyses with the use of fragments of the 16S rRNA and cytochrome b genes also distinguish the new species from individuals in the Kyushu population. The new species has been found in only seven artificial ponds, with approximately 80 clutches of eggs found each year. This endangered species might have the smallest distribution of all those in the genus Hynobius.