This review focuses on the eastern oyster Crassostrea virginica and its pathogen Perkinsus marinus, but the reference points considered are applicable to a wide range of sessile hosts suffering significant mortality from disease. The biological characteristics and imperatives that constrain the deduction of reference points are first reviewed. This is followed by a review of the various models and their reference points that have been implemented or considered in an effort to sustainably manage C. virginica stocks. The last section evaluates the application of reference points addressing maximum sustainable yield (msy) as management tools. Characteristics and imperatives include the preference of abundance over biomass or biovolume as the primary metric for the stock and the bipartite partition of the mortality rate into natural mortality and the additive portion contributed by disease that depends upon the distribution of the stock over the salinity gradient. Other contributing factors include female biases in natural mortality and fishery landings, application of a Ricker model for the broodstock-recruitment relationship, the influence of disease on the surplus production trajectory of the stock, and the importance of managing shell as well as live oysters. Reference points may be developed to manage the disease or the diseased stock. All reference points used in management at this writing are of the latter type. One is volume based; the remainder are abundance based. Constant-abundance reference points have received most attention. Reference points focused on msy have received little use. Constant-abundance reference points stabilize the stock at a known (usually the present) state. Constancy reference points can be applied to the management of the stock and also to the management of the shell resource critical to maintenance of reef habitat. The alternative msy approach is used to stabilize the stock at a state maximizing sustainable production. Though little used, consideration of the behavior of surplus production formulations suggests that msy-based reference points may be feasible and that this approach could then be used to identify management goals other than the present state.