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Delaware's Inland Bays comprise a large estuarine system with a restricted access to the Atlantic Ocean (Indian River Inlet). As part of a local oyster stock enhancement and restoration effort, we conducted a survey for the protozoan pathogen Perkinsus marinus (Dermo) in oysters from a newly established reef. Using standardized methods for the polymerase chain reaction (PCR) amplification of the non-transcribed spacer (NTS) region, we were surprised to find no detectable titers of this pathogen in the 30 oysters sampled in the first year of the project. The detection threshold of the PCR coupled with chemiluminescent detection was 30 fg P. marinus NTS DNA. We were able to detect a trace presence of this pathogen in a few hard clams (Mercenaria mercenaria) from the same locale, indicating that a Perkinsus sp. was present in the Inland Bay system. Subsequent monitoring of the reef system using a fluid thioglycollate assay over 3 yr revealed no epizootic outbreaks of this pathogen within the planted oyster population. Two large mortality episodes that did appear in the oyster population were attributable to abiotic conditions and not pathogen exposure. This study emphasizes that all potential sources of mortality in the environment are important to consider when designing oyster seeding projects. In the Delaware Inland Bays, P. marinus does not appear to have a large enough oyster host population to become a significant disease threat at present. Because of the low parasite incidence levels in the Inland Bay system in 2000, the James Farm oyster reef restoration project presents an ideal model system to follow the population dynamics between an oyster-host population and a latent or reservoir pathogen population. [ABSTRACT FROM AUTHOR]