The completely sequenced mitochondrial genome of the brown marmorated stink bug, Halyomorpha halys, is a circular molecule of 16,518 bp with a total A+T content of 76.4%. Nucleotide composition and codon usage of this genome are near the means observed in other 12 hemipteran mitochondrial genomes; however, the initiation codon for CO1 gene appears to be TTG, dissimilar to what has been seen in the 12 mitochondrial genomes. In this genome, the A+T rich region between srRNA and tRNAIle gene includes two extensive repeat regions, in which each region includes 4 and 12 tandem repeats of a 73 bp sequence, respectively. The gene content, order, and structure of the H. halys mitochondrial genome are consistent with that of Triatoma dimidiata, belong to the same suborder Heteroptera, but different from two suborders, Auchenorrhynca and Sternorrhyncha, including various gene rearrangements. Analyzing phylogenetic relationship and comparing gene order and content of the 13 hemipteran mitochondrial genomes of three suborders, Heteroptera, Auchenorrhynca, and Sternorrhyncha, supported the morphology-based current hypothesis that both Auchenorrhynca and Sternorrhyncha are a monophyletic group.