Bay scallops (Argopecten irradians Lamarck) are ecologically important in U.S. Atlantic waters off northeastern states and in the Florida Gulf of Mexico, and have been intensely harvested from both of those regions for decades. However, a detailed study comparing their basic population genetic structures using more than a single type of genetic marker has not been conducted. Through such a study, key phylogeographic, taxonomic, and fisheries issues can be addressed. We used variation in allozyme loci and mitochondrial DNA restriction fragment length polymorphisms to evaluate and compare the population genetic structures of bay scallops from those two regions, to propose a new interpretation for the composition of the North Carolina bay scallop population, to resolve the taxonomic quandary of Argopecten irradians taylorae, and to evaluate the apparent and potential genetic effects of the common fishery practice of hatchery-based stock enhancement on the genetic diversity and relatedness of Atlantic bay scallop populations. Atlantic Ocean (North Carolina through New York) bay scallop populations are genetically more distant from each other than are Florida Gulf bay scallop populations, except those in Florida Bay. Each Atlantic population has a different phylogeographic history, is quasi-independent, and should be treated as a genetically unique entity. The North Carolina bay scallop population is composed of Argopecten irradians irradians individuals, but also has genetic input from Argopecten irradians concentricus. Bay scallops occurring in Florida Bay constitute a population of A. i. concentricus that has diverged from other Florida Gulf populations because it has undergone repeated contractions and expansions of varying magnitude and is nearly isolated from other bay scallop populations. For the common practice of hatchery-based stock enhancement in the Atlantic, broodstock bay scallops should be taken from the same genetic population, and all stock enhancement efforts should include comprehensive genetic monitoring programs. In some cases, improving the abundance and density of bay scallop aggregations through habitat improvement may be preferable to stock enhancement for bay scallop restoration, but in other cases genetically conscientious stock supplementation or restoration may be the only alternative.