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North American green sturgeon (Acipenser medirostris) display the distinctive behavior of long ocean migrations along the west coast punctuated by summer residence in estuaries; however, little is known about stock composition in these tidal environments. Pairwise comparisons and genetic clustering analysis were used to characterize the two green sturgeon Distinct Population Segments (DPSs) from 20 collections using eight tetrasomic and two disomic microsatellite loci. The observed pattern of green sturgeon DPS composition among five estuaries in California, Oregon, and Washington was supported with assignment testing approaches utilizing the same genotypic data in codominant polysomic and pseudodominant allele phenotype formats. The majority of individuals in northern DPS estuaries originated from the threatened Southern DPS, except in Winchester Bay and Grays Harbor. We detected few Northern DPS green sturgeon in San Pablo Bay, the principal Southern DPS estuary, supporting that green sturgeon preferentially disperse north once they enter their coastal migration. Our genetic findings suggest that stock complexity in green sturgeon is pervasive and support precautionary, interjurisdictional approaches for managing green sturgeon beyond rigid, regulatory boundaries. [ABSTRACT FROM AUTHOR]