The fishery of inshore hagfish (Eptatretus burgeri) is particularly important from the perspective of the eel-skin leather industry in the northwest Pacific. In order to reveal the genetic diversity and population structure of E. burgeri in the northwest Pacific, we analyzed partial nucleotide sequences of three mitochondrial DNA regions (523 bp in COI, 712 bp in ND4 and 617 bp in Cytb) based on specimens collected from six locations in Korea and Japan. The genetic diversities of E. burgeri were higher in Korean locations compared to Japanese ones. AMOVA showed that E. burgeri was completely separated into two groups (group A: southern coast of Korea and western coast of Japan vs. group B: eastern coast of Japan). Furthermore, groups A and B were divided into each two lineages (lineage I: west southern coast of Korea, lineage II: east southern coast of Korea and western coast of Japan, lineage III and IV: eastern coast of Japan). Our molecular results suggest that these two groups and lineages of E. burgeri may be different evolutionary significant unit and management unit, respectively.