Pyemotes zhonghuajia Yu, Zhang & He (Acari: Pyemotidae) is an ectoparasitic mite that efficiently controls agricultural and forestry pests in Lepidoptera, Coleoptera, and Hymenoptera. A single P. zhonghuajia mite can paralyze and kill a host 680,000 times its own weight within 3 h. Although this mite is an efficient and broad-spectrum natural enemy unique to China, its mitochondrial genome is still unknown. In this study, the complete mitochondrial genome of P. zhonghuajia was sequenced and annotated. The complete mitogenome of P. zhonghuajia was 14,772 bp and comprised 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one control region. The base composition of the complete mitogenome was 39.6% of A, 13.1% of G, 7.0% of C, and 40.2% of T, with a total A+T content of 79.8%. The length of 13 PCGs was 10,469 bp, with an A+T content of 78.4%. The length of 22 tRNA genes ranged from 45 bp to 67 bp. The secondary structures of 22 tRNA genes were predicted, and 10 tRNAs had the typical cloverleaf secondary structure, whereas 12 tRNAs were truncated without the D-arm. The 16s-rRNA and 12s-rRNA genes were 1,011 bp and 612 bp, respectively. The control region was 692 bp. The mitogenome gene order of P. zhonghuajia was not consistent with the pattern of its ancestor Parasitus wandunqingi. A phylogenetic tree was constructed using 13 PCG sequences from 29 mites, and the results confirmed that P. zhonghuajia is a species in Eleutherengona.