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Messor structor (Latreille, 1798) is a keystone ant species in the genus Messor (Formicidae: Myrmicinae). Here, we reported the complete mitochondrial genome of M. structor. The circular mitogenome of M. structor is 17628 bp including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region. The base composition was AT-biased (84.07%). Phylogenetic analysis suggests that it is closely related to Aphaenogaster famelica. The mitochondrial genome of M. structor will be a good source for understanding molecular evolutionary studies of this species and related ant species.