Agehana maraho (Shiraki and Sonan, 1934) is a near-threatened swallowtail butterfly endemic to Taiwan. As a first step in evaluating the most variable molecular markers for further population genetic and conservation studies of this and other insects, the entire mitochondrial genome (mitogenome) was sequenced (16,094bp). The most distinctive structure of the Agehana mitogenome is the control region (CR; 1,270bp). This is the longest CR found so far in any lepidopteran, and it also represents the first known case of two units of macro repeats within a tandem region. In a comparison with another 12 lepidopteran mitogenomes, the genes atp8, atp6, and nad6 were found to be more variable than cox1, suggesting an undue focus on cox1 (COI) in identification and phylogeographic studies. A combination of these first three genes plus the CR, comprising micro as well as macro repeats, may thus provide more suitable markers for conservation genetic studies, not only of this near-threatened species, but also of many other insects.