Objective To monitor and analyze the hygienic status of aquatic products in Shenzhen in order to understand the pollution of aquatic products. Methods 345 aquatic samples including fish, shellfish and other aquatic products were collected by random from restaurants, fairs and supermarkets in Shenzhen from 2006 to 2008. Hygienic evaluation was based on the results of testing items including heavy metals, pesticides, pathogenic bacteria, clonorchis sinensis and vibrioparahaemolyticus etc. Results The pollution rates of aquatic products were 8.62%, 3.09% and 20.19% in 2006, 2007 and 2008 respectively. The main pollutant items were vibrioparahaemolyticus, lead and nitrite, and the qualified rates of main polluted fish breeds were 47.37% in grass carp, 25.93% in freshwater grouper and 25% in carp. The contents of shellfish toxin were not exceeded the standards in 7 samples. The pollution rates of clonorchis sinensis were high, 20% in grass carp, 17.14% in tilapia and 12% in crucian. Conclusion The hygienic inspection and guidance for cultivating, marketing and consuming aquatic products should be enhanced. In order to ensure the food safety for consumers, reducing the intake of raw or undercooked aquatic products is necessary.