Abstract: The objectives of the present study were to examine sequence variation in the mitochondrial NADH dehydrogenase subunit 1 (nad1) gene and NADH dehydrogenase subunit 4 (nad4) gene among Coenurus cerebralis isolates in Hunan Province，and to reconstruct their phylogenetic relationship using nad1 and nad4 sequences. The partial nad1 (pnad1) and nad4 (pnad4) were amplified from each C. cerebralis， and pnad1 and pnad4 sequences were aligned using the ClustalX 1.81. MP, and NJ trees of pnad1 and pnad4 were constructed using the software Phylip 3.67 version 4.0 and Mage version 4.0, and ML tree was also constructed using Puzzle version 5.2. Sequence homology analysis was performed using the Megalign program of the software DNAStar version 5.0. The results showed that the lengths of pnad1 and pnad4 sequences were 666 bp and 887 bp, respectively. The constructed phylogenetic tree revealed that the Hunan isolates and the Taenia multiceps available in GenBank were clustered in the same clade. There is no significant variation in pnad1 and pnad4 sequences within C. cerebralis, while interspecies difference is obvious. It is concluded that pnad1 and pnad4 sequences can be used as genetic marker for population genetic studies of cestodes. The results of the present study provided foundation for further studies of molecular epidemiology of C. cerebralis，and for diagnosis of the resultant disease.