Shellfish is one of important vehicles for dissemination of food-borne pathogens. The incidence of food-borne diseases increases every year. Therefore, monitoring and control on the food safety of shellfish is a significant public health concern worldwide. In recent years, our group has studied the pathogens in molecular detection, bioaccumulation and control in shellfish. Based on the our previous studies, the purpose of this article was to provide a review on the pathogens in shellfish in four aspects: the detection methods, distribution, depuration and epidemiology. The molecular methods were widely used in detection of pathogens in shellfish. In addition, the pathogens were bio-accumulated in the gills and digestive glands, including stomach and digestive diverticula, which are good candidate sites for detection of pathogens.