Hexabromocyclododecane (HBCDD) concentrations were investigated in surface sediments, core sediments, and oysters collected from densely concentrated oyster farms in the Geojae-Hansan Bay. HBCDD concentrations in surface sediments, core sediments, and oysters were 14.0~97.6 ng/g-dry, 0.46~59.8 ng/g-dry, and 0.53~1.32 ng/g-wet, respectively. The levels of HBCDDs in the inner bay, in an area with a high density of oyster farms, were higher than those in the outer bay. The HBCDD concentrations in the marine sediments in this study were comparable to or higher than those in industrialized and urbanized coastal areas in Korea. The HBCDD concentrations in the core sediment increased from the 5 cm layer (from the late 1990s) to the surface layer. Recent inputs to the bay may be associated with the increased use of HBCDDs in Korean farming activities. Of the HBCDD isomers, γ-HBCDD was dominant in marine sediments because it is a major isomer of commercial technical mixtures and expanded polystyrene buoys. In contrast, the oyster samples were dominated by α-HBCDD due to its higher assimilation efficiency and longer half-life relative to other isomers. A human health risk assessment for HBCDDs via oyster consumption for the Korean population was carried out, and the risk was very low.