Hemiptera make up the largest nonholometabolan insect assemblage. Despite previous efforts to elucidate phylogeny within this group, relationships among the major sub-lineages remain uncertain. In particular, mitochondrial genome (mitogenome) data are still sparse for many important hemipteran insect groups. Recent mitogenomic analyses of Hemiptera have usually included no more than 50 species, with conflicting hypotheses presented. Here, we determined the nearly complete nucleotide sequence of the mitogenome for the aphid species of Rhopalosiphum padi using RNA-seq plus gap filling. The 15,205 bp mitogenome included all mitochondrial genes except for trnF. The mitogenome organization and size for R. padi are similar to previously reported aphid species. In addition, the phylogenetic relationships for Hemiptera were examined using a mitogenomic dataset which included sequences from 103 ingroup species and 19 outgroup species. Our results showed that the seven species representing the Aleyrodidae exhibit extremely long branches, and always cluster with long-branched outgroups. This lead to the failure of recovering a monophyletic Hemiptera in most analyses. The data treatment of Degen-coding for protein-coding genes and the site-heterogeneous CAT model show improved suppression of the long-branch effect. Under these conditions, the Sternorrhyncha was often recovered as the most basal clade in Hemiptera.