Amblyomma javanense is an important ectoparasite of Manis javanica, although the population genetics, molecular biology and systematics of A. javanense remain poorly understood. In the present study, the mitochondrial genome of A. javanense was sequenced using the Illumina HiSeq sequencing platform (Illumina, San Diego, CA, U.S.A.) and compared with the genomes of two closely related species: Amblyomma fimbriatum and Amblyomma americanum. The intraspecies and interspecies relationships of A. javanense and another 21 selected species were invest...