Objective To understand the infection characteristics and the correlation of the intestinal diarrhea virus with the contamination distribution in marine shellfish and the cases of foodborne diarrhea in Zhoushan City, and provide effective suggestions and measures to prevent and control foodborne diseases. Methods Real-time polymerase chain reaction (PCR) was used to determine Norovirus (NoV) type Ⅰ/Ⅱ, Rotavirus(RV), Sapovirus(SPV), Astrovirus(AsV) and Enteric adenovirus(AdV) from 466 marine seashells and 422 foodborne diarrhea samples. Results About 18.03%(84/466)of 466 seashell samples were positive, among which 4.08%(19/466)were NoV GⅡ, 9.67%(45/466)were SPV, 2.79%(13/466)were AsV and 1.50%(7/466)were AdV. The most detected virus were NoV GⅡ and SPV, mainly, in spring and winter. The highest positive rate (24.75%,25/101) was detected in oyster from retail markets and the lowest positive rate (10.12%,17/168) was in blood clams from aquatic farm. There were statistically significant differences in the positive rates of different viruses and the positive rates of shellfish from different sources and seasons(P＜0.05). About 15.64%(66/422)of 422 seashell samples were identified positive, among which 4.74% were NoV(20/422, mainly GⅡ), 4.74%(20/422)were RV, 3.55%(15/422) were SPV. The most detected virus were NoV GⅡ, RV and SPV, mainly, in spring and winter. The positive detection rate of different viruses and the positive rate of virus in different seasons were statistically different(P＜0.05). Conclusion The pollution situation of intestinal diarrhea virus in marine seashells of Zhoushan was severe, which had correlation with the viral infection characteristics in the foodborne diarrhea cases, according to the same prevalence seasons and main virus types.