Oyster culture, which is a large part of the North American aquaculture industry, is greatly hindered by the parasite Perkinsus marinus. The different oyster defense mechanisms and how the parasite seems to evade them are not fully understood, and the role of apoptosis as an oyster defense mechanism remains unclear. Apoptosis of eastern oyster (Crassostrea virginica) hemocyte subpopulations (granulocytes and hyalinocytes) was quantified at the single cell level using flow cytometric Annexin-V and TUNEL assays. The influences of habitat salinity (540 mOsm [18.9‰] and 910 mOsm [31.9‰] for oysters and 488 mOsm [17.1‰] and 810 mOsm [28.4‰] for P. marinus) and temperature (14.5°C and 25°C for oysters, 14.4°C and 22.5°C for P. marinus) on apoptosis frequencies were evaluated experimentally on the host hemocytes and the parasite. Apoptosis frequency was higher in granulocytes than hyalinocytes, regardless of temperature or salinity. Salinity affected apoptosis of granulocytes and hyalinocytes, with more apoptosis at 910 mOsm than at 540 mOsm (at 14.5°C and 25°C). Parasite apoptosis frequency was significantly higher on culture at the low salinity (488 mOsm) at both low and high temperatures (14.5°C and 22.5°C). Temperature did not significantly affect either hemocyte or parasite apoptosis frequencies. Investigation of apoptosis as an oyster defense mechanism and how temperature and salinity affect C. virginica and P. marinus apoptosis may lead to a better understanding of host/parasite interactions and the mechanisms leading to disease susceptibility or resistance. Such information could lead to better management strategies that may result in reduced disease morbidity and mortality for oyster producers.