New sequencing technologies are providing a large-scale proliferation of sequence data, including complete mitochondrial genomes as a side effect of target capture methods. In this study, we use massively parallel sequencing to provide the nearly complete mitochondrial genome of the ant Octostruma stenognatha. The annotation of the genome revealed an interesting pattern that agrees with a recent deep reorganization in the systematics within the Formicidae family. This is the first mitogenome for the genus in a lineage, where the scarcity of mitochondrial information has restricted our understanding of its evolutionary history. This is a valuable example of the power and velocity with which products from new sequencing technologies can increase our capacity to understand evolutionary biology, especially in non-model species.