Different from the true oyster (family Ostreidae), the molecular diversity of the gryphaeid oyster (family Gryphaeidae) has never been sufficiently investigated. In the present study, the complete mitochondrial (mt) genome of Hyotissa sinensis was sequenced and compared with those of other ostreoids. The total length of H. sinensis mtDNA is 30,385 bp, encoding 12 protein-coding-genes (PCGs), 26 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. The nucleotide composition and codon usage preference of H. sinensis mtDNA is similar to that of H. hyotis within the same genus. On the other hand, the presence of three trnM and three trnL genes of H. sinensis was not detected neither in H. hyotis nor other ostroid species. Another unique character of H. sinensis mtDNA is that both rrnS and rrnL have a nearly identical duplication. The PCG order of H. sinensis is identical to H. hyotis and the two congener species also share an identical block of 12 tRNA genes. The tRNA rearrangements mostly happen in the region from Cox1 to Nad3, the same area where the duplicated genes are located. The rearrangements within Gryphaeidae could be explained by a 'repeat-random loss model'. Phylogenetic analyses revealed Gryphaeidae formed by H. sinensis + H. hyotis as sister to Ostreidae, whereas the phylogenetic relationship within the latter group remains unresolved. The present study indicated the mitogenomic diversity within Gryphaeidae and could also provide important data for future better understanding the gene order rearrangements within superfamily Ostreoidea.