Ceriagrion nipponicum (Odonata: Coenagrionidae) is listed as climate-sensitive indicator species in Korea and now expands its range northward. In this study, we sequenced complete mitochondrial genome (mitogenome) of the species collected from South Korea for comparatively analysis in damselflies and to detect the genes suitable for subsequent population genetic study. Comparison of the mitogenomes from two geographic samples of C. nipponicum showed the highest variation in ND4 and ND1, whereas no variation was detected in COI, warranting usefulness of the two genes for subsequent population-level study. Phylogenetic analysis using 13 PCGs and 2 rRNAs in Zygoptera showed non-monophyletic Coenagrionidae, forming two groups.