Hipparchia autonoe belongs to the family Nymphalidae (Lepidoptera) and is designated as an endangered insect and national monument in Korea. It only inhabits a very restricted area on Mt. Halla but is widely distributed in several Asian countries including Mongolia. A previous study conducted to understand the genetic relationship between Mt. Halla and Mongolian H. autonoe for conservation purposes suffered from a limited number of samples. Therefore, we sequenced the DNA barcode region of an additional 36 H. autonoe individuals, combined them with previous data from 19 individuals, and performed phylogenetic and population genetic analyses. Furthermore, the internal transcribed spacer 2 (ITS2) region was also sequenced from the 36 samples as a nuclear DNA marker. The existence of independent haplotypes, sequence types, and significant FST estimates (p < 0.05) between Mt. Halla and Mongolian populations indicated hampered gene flow between the populations. Nevertheless, an absence of a reciprocal monophyletic group in Mt. Halla and Mongolian populations by cytochrome oxidase subunit I gene- and ITS2-based phylogeny suggests that the genetic isolation of the Mt. Halla population from the Mongolian populations seemed not large enough to consider them independent genetic entities.