Abstract: The complete mitochondrial genome of Hyriopsis schlegelii was obtained by using polymerase chain reaction (PCR), shot-gun sequencing. The genome contains 15939 base pairs and 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 28 non-coding regions ranged from 1bp to 393bp in size. Most genes were encoded on the L strand, while ND3-ND5, ND4L, ATP6, ATP8, COX1-COX3, tRNA-D, and tRNA-H were encoded on the H strand. The structure and organization of mitochondrial genomes of H. schlegelii and other 7 freshwater mussels were analyzed by using comparative genomics and bioinformatics methods. Results showed that: (i) Strong bias was toward A+T for the genome of H. schlegelii. (ii) The striking mitochondrial genome difference in the size performed on the non-coding regions in all the freshwater mussels. (iii) The gene arrangement of H. schlegelii was identical to that of Hyriopsis cumingii and Lamprotula leai, but was different from that of Cristaria plicata, Lampsilis ornate, Pyganodon grandis, Quadrula quadrula and Venustaconcha ellipsiformis between COX2 and 12S rRNA. The difference was caused by rearrangement of 8 genes, including ND3, tRNAHis, tRNAAla, tRNASer1, tRNASer2, tRNAGlu, ND2 and tRNAMet. (iv) Protein-coding genes contained 4 initiation codons which were I (AUU, AUC), V (GUG), M (AUG), and L (UUG) and 13 genes have complete stop codons (UAA or UAG). (v) 22 tRNAs had typical cloverleaf structure. There were an ORF region between tRNA-E and tRNA-W but no control region. The MP-tree based on mtDNA genomes showed the evolutionary position of H. schlegelii relative to that of 14 other bivalvia species. The result showed that H. schlegelii and H. cumingii had the closest relationship than others. The results of this study provide the basis for gene rearrangement and evolutionary characterization of mitochondrial genome in bivalves.