AbstractManagement of Atlantic cod Gadus morhua in U.S. waters is based on a two‐stock model composed of stocks from (1) the Gulf of Maine (GOM) and (2) Georges Bank (GB) and areas south; however, evidence suggests a more fine‐scale structuring. We used microsatellite and single nucleotide polymorphism (SNP) analyses to investigate the stock structure of Atlantic cod in U.S. waters. In year 1, we analyzed microsatellite loci in larvae from GB, age‐0 juveniles from multiple locations in the GOM, and adults of unknown maturity from GB, Jeffreys Ledge, and the Great South Channel (GSC). In year 2, Atlantic cod collected from spawning aggregations in Ipswich Bay in the spring and at GB, Stellwagen Bank, Chatham, and Ipswich Bay in the winter, along with adults of unknown maturity from Long Island, New York, were surveyed at a modified battery of microsatellites and three SNPs. In year 1, we saw no significant differences in allelic frequencies between our composite sample of adult and juvenile cod from the GOM and that from GB nor between the collections from the GSC and any other site. However, a composite sample of juveniles from Massachusetts Bay was significantly different from the GB collection and juveniles from Maine. In year 2, we found highly significant differences in allelic frequencies between Atlantic cod collections from the GOM and GB. The spring collection from Ipswich Bay was highly distinct from the collection from GB and all other sites, including the winter‐spawning Ipswich Bay collection. The Long Island sample was genetically distinct from the GB and the spring collections from Ipswich Bay, but not from other collections. Our study indicates that there is genetic heterogeneity of stocks in U.S. waters, but its structure is complex and to better understand it many more spatially and temporally separated samples must be characterized.