Aquaculture is a fast growing industry in the Northeast United States. Nevertheless, two pathogens, Haplosporidium nelsoni (MSX) and Perkinsus marinus (Dermo), have had devastating effects, killing up to 80% of the harvest. The relationship between the parasites and the oyster defense mechanisms is unclear. Phagocytosis of MSX is rare, while Dermo is phagocytized without destruction. Few studies have attempted to evaluate oysters defense mechanisms, and usually at the level of populations of cells and often indirectly. In order to better understand oyster immunology, to further define the pathogenesis of infectious diseases, we used flow cytometry to directly quantify oysters’ immune functions at the individual cell level. Forward and side-scatter demonstrates three populations of hemocytes: granulocytes, agranulocytes, or hyalinocytes, as well as an intermediate population. Fluorescent latex microspheres allowed us to quantify phagocytosis, which occurs rapidly and peaks at 24 hours. The respiratory burst, as evaluated by the production of peroxides using the probe DCFDA, peaked at 30–60 minutes at 4°C. These assays will allow sorting of hemocytes according to functional properties for the production of monoclonal antibodies that will help determine the phylogeny of hemocytes. The characterization of defense mechanisms in oysters will allow further study of the pathogenesis of economically important diseases, and define the basis for resistant oysters.