Scale insects comprise a diverse group of insects within superfamily Coccoidea in the suborder Sternorrhyncha, many of them are important pests of economic crops. The advent in next-generation sequencing (NGS) technologies has revolutionized conventional phylogenomic researches, causing a rapid accumulation of sequenced insect mitochondrial genomes. However, there have been few studies on the mitochondrial genome of diverse scale insect groups. By using NGS methods, the complete mitochondrial genome of Nipponaclerda biwakoensis was obtained in this study, representing the first mtDNA of the family Aclerdidae. The whole mitochondrial genome is 16,654 bp in length with an A+T content of 81.3%, including 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 17 transfer RNAs and a control region. All PCGs begin with typical ATN codons and use standard TAA as their termination codons, except nad1 gene stopping with TAG. Meanwhile, this mitochondrial genome shows a unique gene rearrangement with a long fragment (trnP-trnC-trnI-nad2-trnY-trnT) insertion in the conserved region nad6-cob, which is novel to Hemiptera, even Insecta. The phylogeny reconstruction of Sternorrhyncha based on 13 PCGs and 2 rRNAs under Bayesian Inference method support a robust topology that Aleyrodoidea is the earliest branch of Sternorrhyncha, with Psylloidea as the sister group of the (Aphidoidea?+?Coccoidea) clade.