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The complete mitochondrial genome (mitogenome) of the Bactrocera cheni (Diptera: Tephritidae: Dacinae) are sequenced and annotated. The mitochondrial genome is 15,945 bp (GenBank No. MN883026), with A + T% for the whole sequence = 73.0% (38.9% A, 16.4% C, 10.6% G, and 34.1% T), which is the classical structure for insect mitogenome. All PCGs started with ATN except ATP8; 9 PCGs use TAA as the stop codon, and others use TAG as the stop codon. The phylogenetic tree confirms that B. cheni and B. tsuneonis are not clade into one branch with strongly supported. And Pairwise Identity is 80.0% between B. cheni and B. tsuneonis. Based this study, we supported that B. cheni and B. tsuneonis are two different species clearly.