Abstract: Based on the Illumina HiSeq platform sequencing technology,the mitochondrial genome double-end sequencing,gene splicing,annotation and gene structure analysis of Bactrocera (Zeugodacus) atrifacies were performed to determine the mitochondrial genome and structural characteristics of B.atrifacies. The phylogenetic tree was constructed using the maximum likelihood method (ML) to analyze its genetic relationship and phylogenetic development. The results showed that the total length of the mitochondrial genome sequence was 15866 bp (GenBank accession number : MW892727),with 37 genes(including 13 protein-coding genes,22 tRNA genes,2 rRNA genes) and 1 non-coding region. Among the codons of 22 amino acids of 13 protein-coding genes,UUA (TTA (leucine)) had the highest frequency N and relative codon RSCU,with N (RSCU) of 378 (3.75). In the secondary structure of tRNA gene,except for phenylalanine (F) lacking pseudouracil (T) ring and serine (S1) lacking dihydrouracil (DHU) ring,the other 20 tRNA genes could fold to form a typical clover secondary structure map. In the mitochondrial tRNA gene,there were 17 base pairs mismatched,and the mismatched base pairs were all G-U ; phylogenetic analysis showed that B.atrifacies and B.(Z.) caudata were closely related and belonged to the subgenus Zeugodacus. The results were consistent with the traditional morphological classification,which provides a basis for further species diagnosis,phylogenetic,evolutionary biology and prevention research.