Abstract: The objectives of the present study were to examine sequence variation in the mitochondrial cytochrome coxidase subunit 1 (cox1) gene and NADH dehydrogenase subunit 1(nad1) gene among Spirometra erinaceieuropaei isolates from Hunan Province，and to reconstruct their phylogenetic relationship using cox1 and nad1 sequences. The partial cox1 (pcox1) and nad1 (pnad1) was amplified from each S. erinaceieuropaei sample，and pcox1 and pnad1 sequences were aligned using the ClustalX 1.81. MP and NJ trees of pcox1 and pnad1 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 pcox1 and pnad1 sequences were 396 and 566 bp, respectively. The constructed phylogenetic tree revealed that the Hunan isolates and the S. erinaceieuropaei available in GenBank were clustered in the same clade. There is no significant variation in pcox1 sequences within S. erinaceieuropaei, while interspecies difference is obvious. It is concluded that pcox1 and pnad1 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 population genetics of S. erinaceieuropaei，and for diagnosis of the resultant disease.