Oyster reefs are one of eleven unique habitats prioritized for restoration in the Hudson River Estuary to improve overall environmental quality and provide society with new and increased benefits from the estuary environment (Miller 2013). This goal is shared by many coastal states and has inspired many supportive breeding programs to revitalize native oyster reefs (Crassostrea virginica) in estuaries across the Eastern United States. In some cases, these programs rely on domesticated aquaculture oyster broodstock to supplement populations with hatchery-produced oysters. However, little is known about the long-term efficacy of supportive breeding using domesticated-strain broodstock vs. adults collected from nature. One basic question is about the degree of genetic difference between these two types of oyster compared with spatial differences among natural stocks. In this study, we collected samples from different life stages (juveniles and adults) of eastern oysters from 10 different sites (N=24 per site) in the Hudson River Estuary and compared them with an aquaculture oyster strain recently used for supportive breeding. Population differentiation was tested at a genomic scale with double digest RADseq data. Among natural population samples there was subtle population structure between the Hudson and East Rivers despite the high dispersal potential present during the 2-3 week pelagic larval stage. This contrast between rivers was seen in both spat and adults, and was consistent across two sampling years. The pattern was most strongly manifest in the highest among-population Fst loci, and became recognizable as a spatially discreet pattern of introgression when the aquaculture strain was included in the analysis. The aquaculture strain showed lower genetic variation relative to wild populations. Until fitness consequences of introgression, and relative fitness of wild and aquaculture oysters can be evaluated over the full oyster life cycle, I recommend stricter adherence to published recommendations that wild broodstock be used for generating oyster restoration seed and to avoid mixed plantings that could facilitate interbreeding.