We have used molecular genetic methods to examine the question of the geographic origins of the newly returned Argopecten irradians populations in Barnegat Bay (BB), New Jersey. Using PCR to amplify specific polymorphic microsatellite regions for bay scallop, we have genetically compared the 2004 and 2005 BB populations to those from Long Island (LI), New York, and North Carolina (NC). Our studies indicate that the 2004 and 2005 BB populations are genetically similar with some allelic frequency differences. Five of the eight loci studied are identical for marker size among BB, LI, and NC populations. The S336 locus demonstrates polymorphic sequences of 138 and 158 basepairs in the NC population that are not observed in LI or BB. The C1832 locus appears identical (122 basepairs) between LI and BB, but demonstrates polymorphisms (132 or 142 basepairs) in the NC population. Additionally, the NC group manifests two further alleles in the M26 locus (135 and 149 basepairs) not seen in BB or LI. These results, along with genetic distance and mean estimated gene flow calculations, support a physical transfer of the Long Island bay scallop larvae down the Atlantic coast to the transition regions around Barnegat Bay.