Objective To investigate infection situation and route of metacercaria of Clonorchis sinensis in freshwater fish in Shenzhen area. Methods Infection rate of metacercaria of Clonorchis sinensis in local imported freshwater fish, freshwater fish were screened and identified by morphology under microscope and PCR. Results There 165 positives out 807 samplse were detected bu microscope with a positive rate of 20.5%. and PCR had identificated 159 positive out of the 807 samples.with a positive rate of 19.7%. The infection rate of Campo was 40.2%,the highest in all kinds of the fish species Clonorchis sinensis were detected in the pigsty and toilets on around the fish -pond, and the first intermediate host of Clonorchis sinensis was also discovered aroundthe fish-pond. Conclusion The infection situation of Clonorchis sinensis in feshwater fish in Shenzhen area is serious, toilet and pigsty built on the fish -pond were major transmission route for Clonorchis sinensis and local people wre infected when eating raw fish.