Measurements of polychlorinated biphenyls (PCBs) were taken in surface sediments inside Seogwipo and Hallim Harbors of Jeju Island, Korea, to evaluate their distribution. These harbors typically have heavy ship traffic. The samples were collected three times (in June, October, and December, 2013). PCB concentrations in sediments from Seogwipo Harbor were higher than in those from Hallim Harbor, but both levels were very low, compared with those in other parts of the world. Sedimentary PCB levels had a strong correlation with organic carbon and fine granule mud content. PCB concentration values in the examined surface sediments were much lower than Sediment Quality Guidelines (SQGs) such as ER-L (Effect Rrange-Low), TEL (Threshold Effects Level) and ISQG (Interim Sediment Quality Guideline)-low value applied in countries, such as USA, Canada, and Australia. This suggests that the PCBs did not have significant biological effects on benthic organisms in the marine environment.