Ectomomyrmex javanus Mayr, 1867 is the biggest Ponerine ant in Korean peninsula. We have determined mitochondrial genome of E. javanus. The circular mitogenome of E. javanus is 15,512 bp long including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a large non-coding region of 822 bp. The base composition was AT-biased (83.8\%). Gene order of E. javanus is identical to Cryptopone sauteri belonging to Ponera genus group which is same to that of E. javanus. Phylogenetic trees show that E. javanus is sister to C. sauteri and both species are outside of the remaining ant mitogenomes agreeing with current phylogeney. The mitochondrial genome of E. javanus will be a milestone for understanding E. javanus in the aspect of molecular phylogeny.