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The order Microcoryphia, commonly known as bristletails, is considered as the most primitive one among living insects. Within this order, two species, <i>Coreamachilis coreanus</i> and <i>C. songi</i> (Machilidae: Machilinae), display the following contrasting reproductive strategies: parthenogenesis occurs in <i>C. coreanus</i>, whereas sexual reproduction is found in <i>C. songi</i>. In the present study, the complete mitogenomes of <i>C. coreanus</i> and <i>C. songi</i> were sequenced to compare their mitogenome structure, analyze relationships within the Microcoryphia, and assess adaptive evolution. The length of the mitogenomes of <i>C. coreanus</i> and <i>C. songi</i> were 15,578 bp and 15,570 bp, respectively, and the gene orders were those of typical insects. A long hairpin structure was found between the ND1 and 16S rRNA genes of both species that seem to be characteristic of Machilinae and Petrobiinae species. Phylogenetic assessment of <i>Coreamachilis</i> was conducted using BI and ML analyses with concatenated nucleotide sequences of the 13 protein-coding genes. The results showed that the monophyly of Machilidae, Machilinae, and Petrobiinae was not supported. The genus <i>Coreamachilis</i> (<i>C. coreanus</i> and <i>C. songi</i>) was a sister clade to <i>Allopsontus helanensis</i>, and then the clade of ((<i>C. coreanus</i> + <i>C. songi</i>) + <i>A. helanensis</i>) was a sister clade to <i>A. baii</i>, which suggests that the monophyly of <i>Allopsontus</i> was not supported. Positive selection analysis of the 13 protein-coding genes failed to reveal any positive selection in <i>C. coreanus</i> or <i>C. songi</i>. The long hairpin structures found in Machilinae and Petrobiinae were highly consistent with the phylogenetic results and could potentially be used as an additional molecular characteristic to further discuss relationships within the Microcoryphia.