The population structure and demographic history of a zoarcid fish, Davidijordania poecilimon (Jordan and Fowler, 1902), around Japan were investigated on the basis of sequence variations in the cytochrome b gene of mitochondrial DNA (440 base pairs). Among 44 specimens, 18 haplotypes were recognized. Although some were shared among individuals from different localities in the Sea of Japan or in the Pacific Ocean, no haplotypes were shared between the two regions. The haplotype network showed a rough separation of the Sea of Japan and Pacific population haplotypes, forming a dumbbell-like pattern, each half with a major haplotype. In addition, the pairwise Φ_<ST> between the Sea of Japan and Pacific populations of 0.35 was significant according to the permutation test (p < 0.01). Such evidence indicates that gene flow between the two populations is restricted by the shallow strait (Tsugaru Strait) between the Sea of Japan and the Pacific Ocean. Mismatch distribution analysis suggests that the Pacific population comprises historically older and larger populations than those in the Sea of Japan.