Mitochondrial inheritance mode of some bivalves is different from standard mitochondrial inheritance (SMI), which is named doubly uniparental inheritance (DUI). Hyriopsis schlegelii is a freshwater bivalve, is it DUI? The paper researched the complete mitochondrial genome of male H. schlegelii using PCR, shot-gun sequencing technology, and analysised DUI of mitochondrial genome of H. schlegelii according to the mtDNA characteristics, protein-coding genes, tRNA-His gene and the difference of non-coding region of male and female H. schlegelii. The results show that the mitochondrial genome sequences of male and female contain 15 961 and 15 939 base pairs, respectively. Two mtDNA sequences contain identical genetic constitution and gene arrangement including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 28 non-coding regions ranged from 1 to 393 bp in size. Compared the protein-coding genes of two sequences, there was no difference in sequence length, and the ratios of transition, transversion and amino acid difference were 1.01%-7.34%, 0.00%-0.62% and 0.00%-9.35%. There was 2.72% transition and transversion of COX1 and 7.5% of COX2 between male and female. There was no extra male sequence of a 3′ C-terminus codon extension of COX2. 12SrRNA gene of male contains 5 bp transition and the ratio was only 0.6%; 16SrRNA of male was 9bp longer than that of female and the transition ratio was 1.2%. The location of tRNA-His was the same between male and female, which was encoded on the H strand and was located between COX2 and ND3. There is no control region in non-coding regions. There were identical potential polypeptides in the non-coding regions between tRNA-Glu and tRNA-Tyr of male and female, which were not the male-specific proteins. Constructing a molecular phylogenetic tree based on COX1 genes using neighbor-joining methods (MEGA 4.0 software), the results show that H. schlegelii and Hyriopsis cumingii are the closest relationship than others; male Pyganodon grandis, Venustaconcha ellipsiformis and Quadrula quadrula, which was DUI species, were monophyletic, female were the other monophyletic. In conclusion, there is a litter difference between male and female H. schlegelii. But there is much less different from male and female of other freshwater shellfish and there is probably no DUI about mitochondrial genome in inheritance of H. schlegelii.