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AbstractAtlantic sturgeon Acipenser oxyrinchus oxyrinchus is widely distributed along the Atlantic coast of North America, with spawning populations extending from the St. Lawrence River, Quebec to the St. Marys River, Georgia-Florida. At one time, Atlantic sturgeon supported lucrative fisheries on adults within rivers where they spawned and on subadults and adults within coastal waters. Because of decimated population sizes, Atlantic sturgeon in U.S. waters are now federally protected as five Distinct Population Segments (DPS) under the U.S. Endangered Species Act. While juvenile Atlantic sturgeon are resident within their natal rivers, subadults and adults are highly migratory in coastal waters and often occur in non-natal estuaries, exposing them to a variety of anthropogenic threats outside of their natal estuaries, including bycatch. To most effectively protect the smallest and most vulnerable populations, a method is needed to accurately identify the population origin of individual specimens and their aggregations outside of their natal systems. In this study, microsatellite DNA analysis was used to identify the genetic population structure of Atlantic sturgeon across 13 reference populations. Their genetic profiles then were used to identify the population origin of individuals collected from six coastal locales and one non-natal estuary. All 13 reference collections harbored genetically distinct, and in some cases more than one, population of Atlantic sturgeon. The Hudson River was by far the largest contributor to the overall coastal and non-natal estuarine collections, at 35.3%. The contributions of the other reference populations varied considerably between < 1.0% (York, Edisto, Savannah, and Satilla rivers) to 15.6% (Saint John River) and 12.9% (James River) and appeared unrelated to their estimated population sizes. These results suggest that migratory behavior in marine waters varies greatly among Atlantic sturgeon populations, and should assist resource managers assess the effects of anthropogenic stressors on sturgeon outside of their individual natal river or DPS. [ABSTRACT FROM AUTHOR]