The complete mitochondrial genome of Cultellus attenuates, a new aquaculture species, was sequenced and compared with mitogenomes from seven species of Heterodonta bivalve mollusk in the gene bank. The mitochondrial genome of C. attenuatus is 16888bp in length and contains 36 genes, including 12 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs, and all genes are encoded on the same strand. In comparison with C. attenuates, the mitochondrial genes of the Sinonovacula constricta from the same family were not rearranged, but those of six other species from different family were rearranged to different degrees. The largest non-coding region of C. attenuatus is 1173bp in length and with the A + T content of 68.24%, located between nad2 and trnK. The results of phylogenetic analysis show that the C. attenuates and the S. constricta belonging to Cultellidae cluster into one branch while two species of Solenidae ( Solen grandis and Solen strictus) are clustering as their sister taxon. These data not only contribute to the understanding of the phylogenetic relationship of the Heterodonta, but also serve as a resource for the development of the genetic markers in aquaculture.