Complex interrelationships between biological traits and environmental conditions influence the genomic diversity and population structure of marine species. Offspring of broadcast spawning organisms are subject to oceanographic, benthic, and chemical conditions that influence survival and connectivity, with the potential to produce genomic divergence between populations at closely located sites. This study aims to use restriction site-associated DNA sequencing (RADseq) to characterize fine-scale genomic differentiation between eastern oyster populations in and around Beaufort Inlet, North Carolina. RADseq libraries have been prepared from 29 oysters from each of seven beds in Bogue Sound, Back Sound, North River, and surrounding bodies of water, for coverage of 203 total individuals from a maximum of ~20 km apart. These beds were selected from a geographic area spanning the swift flowing and well trafficked Beaufort Inlet entrance, and additionally represent a range of environmental conditions, including salinities and proximities to intense anthropogenic development. The resulting sequence data will be analyzed to determine genomic differentiation between sites, putative markers of selection, and association between markers of selection and local environmental conditions. This research will help elucidate connectivity patterns of oysters in the area of study as well as provide insights on potential fine-scale genomic adaptation in benthic marine species.