Since the ban of tri-butyl tin, other various alternative antifouling agents have been used. In this study, the contamination levels from these antifouling agents were examined in the main harbors in Korea. The sampled harbors were classified into four types and the levels of contamination from the antifouling agents were analyzed. The highest degree of contamination was found in the big harbors, followed by the fishing harbors, harbors near agricultural areas, and military and coast guard harbors. In addition, an increase in the number of ships that entered the ports significantly influenced the contamination by the antifouling agents. Correlation analysis was conducted to characterize the alternative antifouling agents. The results revealed strong correlations between the dichlofluanid and chlorothalonil, and between the chlorothalonil and TCMTB, because unlike Irgarol 1051 and SEA-NINE 211, which are used only as antifouling agents, chlorothalonil, dichlofluanid, and TCMTB are also used in agriculture.