Eight fecal sterols were analyzed in surface sediments collected from shellfish farming areas in Yeoja Bay and Gangjin Bay, Korea, to evaluate sewage-derived fecal pollution. The concentrations of coprostanol, a good marker of sewage-derived organic contamination, in sediments were in the range of 10-530 ng/g-dry in Yeoja Bay, and 10-190 ng/g-dry in Gangjin Bay. Coprostanol levels were markedly higher in the inner bay than in the outer bay. These levels were lower than those reported in urbanized bays in Korea, however, they were comparable to levels in other shellfish farming areas including Gamak Bay. A multivariate analysis of the ratios of other sterols suggested that the sterols originated from sewage and plankton/benthos. Sewage was the dominant source at stations located close to the river mouth and wastewater treatment plant (WWTP) outfalls, and plankton/benthos was the primary source in the outer bay. These results suggest that management of point sources, e.g., WWTP as well as non-point sources, e.g., riverine inputs is important for improving the water quality in Yeoja Bay and Gangjin Bay.