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 investigated by constructing a maximum‐likelihood tree and a neighbour‐joining tree. The mitochondrial genome of A. javanense was 14 780 bp in length and contained 13 protein‐coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two control regions. The results of the comparisons indicate that there is great similarity among these three species, and both trees indicate that A. javanense is a member of the Amblyomminae. The study of A. javanense of pangolins also indicates the premise and foundation of the relationship between the parasite and other species. This is the first report on the mitochondrial genome of Amblyomma javanense collected from the body surface of the endangered Malayan pangolin (Manis javanica). Illumina HiSeq sequencing technology (Illumina, San Diego, CA, U.S.A.) was used to obtain the sequence of the template DNA fragments of the mitochondrial genome of Amblyomma javanense. There is great similarity among Amblyomma javanense, Amblyomma fimbriatum and Amblyomma americanum, with both trees indicating that A. javanense is a member of the Amblyomminae.