Abstract: Objective To study the genetic variation of two mitochondrial DNA molecules (CO1 and Cytb gene) of Oncomelania hupensis isolated from different areas. Methods Snails were collected from Jingxi of Guangxi，Yueyang of Hunan and Eryuan of Yunnan. Genomic DNA was extracted from the snails，Co1 and Cytb gene fragments were amplified by PCR，then purified and sequenced. Sequences of each isolates were edited by using Clustal W(1.82) software，and the nucleotide composition，transition and transversion were accounted by using MEGA(3.1) software. The genetic distances were computed with Kimura method and phylogenetic trees were constructed with UPGMA and MP method respectively. Results CO1 and Cytb gene fragments were about 700 bp and 600 bp(including 2 primers) respectively. A total of 106 mutation spots (15.9%) were tested in CO1 homological nucleotides，and 165 mutation spots (28.5%) were tested in Cytb homological nucleotides. The distance matrix between Guangxi isolate and Hunan isolate was 0.051 and 0.031 for CO1 gene and Cytb gene respectively；while that between Guangxi and Yunnan isolates was 0.158 and 0.405 respectively. Phylogenetic trees constructed by UPGMA and MP took on the similar topo-structure：isolates of Guangxi and Hunan clustered into one group，while the Yunnan isolate exhibited as another group. Conclusion Oncomelania hupensis in Guangxi，Hunan and Yunnan are of relatively rich polymorphism in CO1 and Cytb genes in general.

Key words: Oncomelania hupensis, CO1 gene, Cytb gene, Gene variation