The Atlantic sturgeon Acipenser oxyrinchus oxyrinchus has a latitudinally broad distribution along the east coast of North America, with extant populations occurring from the St. Lawrence River to Georgia. This large anadromous fish once supported intensive caviar-based fisheries that resulted in overharvest and sharply reduced population abundances; presently, directed commercial fishing for Atlantic sturgeon is banned in U.S. waters. We sequenced a 203-base pair section of the mitochondrial DNA (mtDNA) control region of 332 Atlantic sturgeon speciments from 11river systems across their range to elucidate their stock structure. We found a pronunced latiudinal cline in the number of composite mtDNA haplotypes and in haplotypic diversity that increased from north to south and from previously glaciated and subsequently recolonized systems to the portion of their range which never was glaciated. The number of haplotypes by population ranged from 1 in each of the two northernmost populations to 17 in the Savannah River.  Haplotypic diversity ranged form 0.0 to 0.90. The greater genetic diversity shown by southern populations is most likely a product of the probable continunity of these populations through the Pleistocene and to the faster mutation rates associated with their shorter generation times.  Sixty-four percent of the 39 composite mtDNA haplotypes found were unique to particular populations.  Monomorphism of the two Canadian populations. Monomorphism of the two Canadian populations suggested a strong founder effect. Three haplotypes unique to northern populations were probably the result of base substitutions that occurred within the past 10,000 years. In contrast with an earlier study, we found stock structure among southern populations and evidence of at least seven genetic stocks across the subspecies’ range.