Corbicula fluminea is a common macrozoobenthos in the freshwater of the Hongze Lake, which plays an important role in the cycle of mass and energy fluxes of fresh water ecosystem. However, the wild source of C. fluminea has sharply decreased recently due to over-fishing and water pollution. The genetic diversity of C. fluminea in the Hongze Lake has not been widely investigated. The present study analyzed the genetic diversity of C. fluminea population in the Hongze Lake using mitochondrial DNA cytochrome coxidase subunit Ⅰ (COⅠ) gene molecular marker. The mitochondrial DNA COⅠgene fragments were amplified and sequenced from 50 individuals of wild C. fluminea in the Hongze Lake. The contents of A, T, G and C in the 614-base pair fragments of COⅠgene were 22.6%, 42.4%, 21.0% and 14.0%, respectively, and the content of A+T was significantly higher than that of G+C. Sixty-seven polymorphic sites were detected, accounting for 10.9% of the total sequences, and of which sixty-three were parsimony- informative sites and four were singleton sites. Fifteen haplotypes were defined in 50 individuals of C. fluminea. The mean haplotype diversity, nucleotide diversity, and the average number of nucleotide difference in the C. fluminea population were 0.870, 0.045 and 27.370, respectively. The genetic distance among fifteen haplotypes ranged from 0.002 to 0.095. Neighbor-joining (NJ) and maximum-parsimony (MP) trees divided fifteen haplotypes into two clades, suggesting that C. fluminea populations had significant genetic difference. Mismatch distribution analysis showed a multiple type, and Tajima’s D value (2.724) of neutrality test is positive but significantly different, demonstrating that C. fluminea in the Hongze Lake hadn’t experience a recent population expansion. These results suggest that the genetic diversity of C. fluminea population in the Hongze Lake is high, which provides scientific information for the conservation and sustainable exploitation of C. fluminea.