Abstract: The mitochondrial genomes can provide useful information of the phylogenetic relationships among arthropod groups from two aspects, i.e. gene arrangement and mitochondrial DNA (mtDNA) sequence variation, however, there is no report on the mt genomes of species in the order Poicilostomatoida. The present study aims to determine the nucleotide sequence of mitochondrial geneme of Sinergasilus polycolpus, a poicilostomatoid copepod, parasitizing the freshwater fish Hypophthalmichthys molitrix and Aristichthys nobilis. The segments of Cyt b and CO I genes of S. polycolpus were amplified using the degenerate primers, which were designed on the basis of the homologous sequences. Then the special primers were designed on the above segments to amplify the long mtDNA sequence with Long-PCR. Finally, a mtDNA sequence of 12917 bp in length was gotten from S. polycolpus, and deposited in the GenBank database with the accession number of EU621723. This sequence was composed of A of 35.0%, T of 35.8%, C of 14.0% and G of 15.2%, and furthermore the GC-Skew and the AT-Skew were 0.041 and ?0.011, respectively. According to the sequence homology and the structure characteristics, the total of 35 genes were identified, including one 12S rRNA, twenty-one tRNA and thirteen protein-coding genes. However, the amplification for the segment containing putative 16S rRNA, tRNAArg and tRNAThr genes and control region was unsuccessful. The 13 protein-coding genes had ATA, ATG, ATC and ATT as initiation codons, and TAA, TAG, TA and T as termination codons, respectively. TA and T were incomplete termination codons. All the 21 tRNA genes, ranging between 54 and 63 bp in length, could be folded to form the figure of clover leaf knot. However, other than 3 tRNA genes without TψC arm, the length of TψC arms of tRNA genes varied from 1bp to 4bp. Of 35 genes, 4 protein-coding genes, i.e. CO I, ND5, Cyt b and ND4, and 7 tRNA genes, i.e. tRNALeu(CUN), tRNAMet, tRNAPro, tRNAAsp, tRNAGlu, tRNATyr and tRNAHis, were encoded on the N strand, the remainders on the J strand. In addition, 12 gene overlapping sites were found in the Sinergasilus polycolpus mtDNA, but the significance of gene overlapping in the copepod mt genomes was incompletely clear. In order to elucidate the phylogeny of the copepods, it is necessary to study the mt genomes of more copepods as well as other related groups.