In the Arctic, Arctic cod (Boreogadus saida) is an abundant marine fish that plays a vital role in the marine food web. However, little is known about the distribution of genetic variation across its range. Within Alaskan waters, the physical oceanography of the Beaufort Shelf is influenced by a variety of local and remote processes including atmosphere, adjacent shelves from Chukchi Sea (western boundary) and Canadian Beaufort Sea shelf (eastern boundary), Arctic Ocean basin, and freshwater discharge from coastal rivers which may act as dispersal barriers. In this study, we examined the population genetic structure and identify dispersal barriers of three Arctic-dwelling Gadidae species in Alaska marine waters. We used double-digest restriction-associated DNA sequences (ddRADseq) to identify geographic breaks in genetic structure in Boreogadus saida, Gadus chalcogrammus, and Eleginus gracilis. As the Arctic ecosystem continues to change, distributions will likely shift altering species interactions and potentially species abundance in areas. Changes in distributions may result in new areas of secondary contact and potentially hybridization. Using (ddRADseq), we assessed the level of hybridization between Boreogadus saida and Arctogadus glacialis where the two species overlap in combination with mitogenome data to determine the direction of hybridization events.