The mitochondrial genome of Bactrocera cucurbitae, a representative of the Tephritid family, was completely sequenced for the first time. The B. cucurbitae genome is a double-stranded circular molecule of 15,825 bp long, including the entire set of the 37 genes. The 72.9% A+T content and 0.047 AT-skew are within the range of the known dipteran genomes. Comparative analyses showed that dipteran mitochondrial protein-coding genes present complex evolutionary patterns. Some of the codon families were strongly biased towards J-strand. The mitochondrial ATP8 of B. cucurbitae exhibited a faster substitution rate than other genes. Cox1 is the slowest evolving protein and could be considered as a potential phylogenetic marker.