After total ban on the use of tributyltin (TBT) based antifouling paint in Korea from 2003, alternative antifouling paints (AFPs) have substituted TBT and became emerging contaminants in the marine environment. Some of AFPs has demonstrated high toxicity to plant species. Target AFPs including diuron, sea nine-211, Irgarol 1051, dichlofluanid, pyrithiones (Cu and Zn) and M1 (degradation product of Irgarol 1051) were quantitatively analyzed by LC-MS/MS. Compound and source specific parameters and HPLC conditions were optimized for target AFPs. Multiple reaction monitoring mode (MRM) was used for peak identification and quantitation. Recoveries of spiked AFPs in water samples ranged 82~92%. The instrument detection limit ranged 0.05~50 ng/L in seawater, depending on the individual compounds. Diuron was the most frequently detected biocides in seawater (29.2~1360 ng/L) followed by irgarol 1051 (nd~14.1 ng/L) and sea nine-211 (nd~366 ng/L). However pyrithiones (Cu and Zn) and dichlfluanid concentration were under detection limit. Diuron and irgarol 1051 concentrations in seawater from this study are similar other countries, and lower than maximum acceptable or permissible environmental concentration levels.