Severe over-fishing, habitat degradation, and recent disease impacts have devastated the eastern oyster (Crassostrea virginica) fishery in the Chesapeake Bay. Several restoration efforts are in progress, including the unconventional approach of seeding reefs with an aquaculture strain selected for disease resistance and fast growth in hopes of mitigating the negative effects of disease and low census numbers. Supplementation of four sites (The Great Wicomico, Lynnhaven, York, and Elizabeth Rivers) examined in this study totaled approximately 18,500,000 aquaculture oysters from 2002 to 2006. We collected locally recruited offspring (n = 6517) from 2002 to 2006 at these sites to determine if reproduction by the transplanted oysters produced detectable contributions to recruitment by examining the frequency of a composite mitochondrial haplotype that occurs at high frequencies in this aquaculture strain but is rare in wild Chesapeake Bay oysters. The estimated frequency of this haplotype in locally recruited oysters (average 1.4%, SD = 0.9) was compared with the average frequencies found in the hatchery produced (35.9%, SD = 12.8) and wild (1.2%, SD = 0.9) oysters, but we were unable to refute the null-hypothesis that population supplementation made no contribution to recruitment. We discuss five nonmutually exclusive explanations for the limited impact of supplementation, including unequal sex-ratio, predation, flushing, relative scale, and aquaculture selection. We argue that predation, relative scale, and aquaculture selection are the likely reasons for the limited contribution made by aquaculture oysters used for population supplementation.