Tropilaelaps mercedesae Anderson and Morgan, 2007 (Acari: Laelapidae) is a serious ectoparasite of the brood of several honey bee species. Among the four recognized species of Tropilaelaps, Korean population was renamed as T. mercedesae from T. clareae on the basis of morphological evidences and genetic data. In this study, we report the complete mitochondrial genome (mitogenome) sequence of T. mercedesae. The 15,119-bp long mitogenome has an identical gene arrangement to that of Chinese sample reported previously. Comparison of two geographic samples showed COII, ND5, ND4, ND6, CytB, and ND1 to have higher number of variable sites than COI, which is often used for population-level study, suggesting these genes to have potential usefulness for population genetic study. The mitogenome sequence of T. mercedesae from Korea could be useful for species identification for geographic samples, trace of the origin of local populations, and illustration of evolutionary distinction among Tropilaelaps species either using part of or whole genome.