The fishery of inshore hagfish (<i>Eptatretus burgeri</i>) 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 <i>E. burgeri</i> 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 Cyt<i>b</i>) based on specimens collected from six locations in Korea and Japan. The genetic diversities of <i>E. burgeri</i> were higher in Korean locations compared to Japanese ones. AMOVA showed that <i>E. burgeri</i> 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 <i>E. burgeri</i> may be different evolutionary significant unit and management unit, respectively.