The eastern oyster, Crassostrea virginica, has been an important fishery species in the United States for hundreds of years. The emergence of population devastating diseases such as MSX and Dermo was met with the development of disease-resistant lines. Although selectively bred oysters have shown improved survival and growth under diseases in the field, it is unknown if long-term selection has altered larval fitness. In this study, the larval fitness of a selected line (DBX) was studied and compared with that of the Delaware Bay wild (Wild) population under hatchery and natural conditions with the latter using untreated seawater, 50% feeding, and declining salinity. No difference in growth was observed between DBX and Wild larvae under either condition, but DBX exhibited a higher survival under hatchery conditions (P = 0.090), whereas the Wild performed equally well under both conditions. Under natural conditions, the DBX larvae had higher survival during the first week when the salinity was high, but lower survival later under low salinity. The DBX larvae had a much higher setting success and a preference for oyster shells as substrate compared with the Wild larvae. Results of this study indicate that selective breeding has unintentionally altered larval fitness of DBX and led to adaptation to hatchery and high salinity conditions with greater setting success, and the Wild larvae have wider adaptability to different conditions. These findings suggest that careful evaluation is needed to fully assess the recruitment potential of selected stocks used in aquaculture and restoration.