In order to understand the distribution of organic matter and heavy metal concentrations in the surface sediments of fishery resources protection areas (FRPAs), we measured the grain size, ignition loss (IL), chemical oxygen demand (COD), acid volatile sulfide (AVS), and concentrations of heavy metals (As, Cd, Cr, Cu, Fe, Hg, Pb, and Zn) in the surface sediments collected at 54 stations of 5 FRPAs (Gamak Bay, Yeoja Bay, Deukryang Bay, Wando coast, and Youngkwang coast) in the southwestern coast of Korea in February 2017. The surface sediments consisted of fine sediment such as mud, with 2.9~8.8Ø (7.4±0.1Ø) of mean grain size. The average concentrations of IL, COD, and AVS in the sediments were 4.63±0.96 %, 13.0±3.1 mgO2/g·dry, and 0.092±0.124 mgS/g·dry, respectively, and were lower for sediments from the Youngkwang coast than those from other FRPAs. The average concentrations of heavy metals in the sediment were 7.5±0.9 mg/kg for As, 0.04±0.02 mg/kg for Cd, 70.2±9.7 mg/kg for Cr, 15.3±2.8 mg/kg for Cu, 3.3±0.5 % for Fe, 0.014±0.003 mg/kg for Hg, 25.0±6.0 mg/kg for Pb, and 99±14 mg/kg for Zn, respectively, and were relatively higher for sediments in the inner bays than those from the outer bays and coasts. Based on the assessment of sediment samples using the sediment quality guidelines (SQGs), the pollutant load index (PLI), and the ecological risk index (ERI), the surface sediments of FRPAs in the southwestern coast of Korea do not appear to be polluted by heavy metals, suggesting that the heavy metal concentrations in the sediments would not adversely impact aquatic and benthic organisms.