This paper focuses on the analysis of effects on fisheries sector following Korea-Japan Free Trade Agreement and the results are found as follows. In terms of national competitiveness, the RCA(Revealed comparative advantage) index shows that Korea is higher than Japan in most species items. And the calculation of TSI(Trade Specialization Index) finds that Korea is export specialized while Japan import specialized, showing that Korean fisheries sector is internationally more competitive than Japan. The tariffs on the marine products should be completely scrapped between Korea and Japan, export of marine products to Japan increases a mere 2%, while import from Japan 13.5%. In terms of value, annual export to Japan stands at 20,135thousand USD, while import from Japan at 12,137thousands USD, resulting in trade balance improvement of 8,000thousand USD in total. The tariff measures above is expected to have a positive effect on the related industry of marine products such as Oyster, Conger eel, Ark shells and Laver, but those involved in fisheries of Alaska pollack, Hair tail, Sea-bream(live fish), Red horsehead(frozen), Saury are expected to be negatively affected. Given the results of analysis above, the effects of FTA on the fisheries would be advantageous to Korea as a whole, but at the same time, the advantage and disadvantage sustained differs by fishery type and marine products. To that effect, negotiation strategies and countermeasures should be made, taking the results into account.