Although the concept of genetic refuge has long been employed in ecological and paleoecological context, it has only rarely been used to identify regions where organisms are protected from diseases that affect the rest of a population. The refuges harbor individuals that have not been exposed to selective mortality and remain susceptible to the disease. They represent a reservoir of susceptibility alleles that can mix with those from resistant survivors of disease and can retard the development of resistance in the population as a whole. Two water-borne protistan parasites affect oysters along the east coast of the United States: Haplosporidium nelsoni (MSX disease) and Perkinsus marinus (dermo disease). Both are sensitive to low salinity and their prevalence is reduced in the upper reaches of estuaries. We investigated the temporal and spatial structure and extent of putative refuges from these diseases in the upper Delaware Bay, USA and their potential to affect the development of resistance in the oyster population. Our results showed that refuges occurred as a continuum of zones, regions where a pathogen (1) was not present; (2) was present, but did not cause observable infections; and (3) caused infection, but neither disease nor mortality. The zones were transient, driven only partly by short-term climatic conditions, and differed according to parasite: H. nelsoni was often not present in the refuges, as inferred by the absence of polymerase chain reaction (PCR) – positive signals on the gills, and when it was present, it did not always cause lethal, or even histologically detectable, infections. In contrast, P. marinus was present in all upper estuary areas sampled, where it caused detectable, although not necessarily lethal-level, infections. Thus, a significant fraction of the oyster population is protected from selective mortality in these refuges even when the parasites are present. An incursion of H. nelsoni into the upper Bay in the 1980s left most of the surviving population highly resistant to MSX disease, although populations in the upper-most reaches are still susceptible. The lack of selection pressure in the refuges likely helps to retard the development of resistance to dermo disease, and theoretically could cause resistance to MSX disease to regress although there is no evidence to date that this has occurred.