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Aphaenogaster japonica (Forel, 1911) is an omnivorous ant that is widely distributed in eastern Asia. The mitochondrial genome of A. japonica reported here was 18,607 bp in length, consisting of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region. The base composition was AT biased (the GC ratio is 18.9%). With A. japonica added, we obtain weak evidence that the sister group of the Stenammini group, including Aphaenogaster, is the Myrmicini group. Therefore, the Stenammini and Myrmicini groups may be not a robust monophyletic group, unlike the previous results based on the complete mitochondrial genome.