The Shellfish Program has two primary missions, public health protection and both direct and indirect management of the Commonwealth's molluscan shellfish resources. Public health protection is afforded through the sanitary classification of all 1,745,723 acres of overlying waters within the states territorial sea in accordance with the provisions of the National Shellfish Sanitation Program (NSSP). The NSSP is the federal/state cooperative program recognized by the U.S. Food and Drug Administration (FDA) and the Interstate Shellfish Sanitation Conference (ISSC) for the sanitary control of shellfish produced and sold for human consumption.

Shellfisheries management is accomplished by direct Division of Marine Fisheries (MarineFisheries) regulation of the commercial surf clam, ocean quahog and quahog dredge boat fisheries, harvest of contaminated shellfish for depuration and relaying, size and maximum harvest limits of other shellfish, Bay scallop and conch seasons, shellfish aquaculture and collection of statistics. Indirectly, MarineFisheries manages through its partnership with the coastal cities and towns by providing technical assistance and through consultation with local management authorities (elected officials and shellfish constables) in the development of management plans and local regulatory decisions.