We sequenced the complete mitochondrial (mt) genome of Camponotus atrox (Hymenoptera: Formicidae) that is distributed only in Korea. This genome is 16,540 bp in size, contains typical sets of genes (13 protein-coding genes, 22 tRNAs, and two rRNAs). The C. atrox A+T-rich region is the longest in the sequenced ants as 1,402 bp and is comprised of an identical tandem repeat consisting of six 100-bp copies and one 96-bp copy. A total of 315 bp of intergenic-spacer sequences were spread over 23 regions. An attempt to align spacer sequences in ants turned out that alignment was mostly feasible among congeneric species, with a substantial sequence divergence, indicating the potential of these sequences as congeneric molecular markers. The A/T content in first and second codon positions of PCGs are similar in ants including C. atrox (73.9 vs. 72.3% on average). Estimation of degree of genetic divergence (e.g. non-synonymous substitution rate) with an increased taxon sampling among hymenopteran superfamilies indicated the presence of different rates of divergence between the suborders Symphyta and Apocrita as has previously been reported. The C. atrox mt genome has a unique gene arrangement, trnI-trnM-trnQ at the A+T-rich region and ND2 junction (underline for inverted gene), possibly originated from tandem duplication of trnM-trnI, resulting in trnM-trnI-trnM-trnI-trnQ and loss of first trnM and second trnI, resulting in trnI-trnM-trnQ.