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Banda Sea waters is the potential area for fisheries, especially for Tuna. Banda eddy and the relationship to chlorophyll-a were studied using the output of ocean circulation model INDESO (Infrastructure Development of Space Oceanography) configuration from 2008-2011 during normal (June-August 2008) and ENSO (El Nino/ June- August 2009 and La Nina/ June-August 2010). The model result showing two clockwise eddies in the northern part of Banda sea and three counterclockwise eddies in the southern part of Banda Sea. The eddy counterclockwise was found from 20 m depth and causing upwelling along the island arc on the western edge of Banda sea. Eddy counterclockwise in the southern of Banda Sea cause the downwelling. The presence of these 5 eddies is thought to be an important factoring in maintaining water balance system in the Banda Sea as long as southeast monsoon period. In the surface, higher vorticity of the eddy was found in the northern of southwest Maluku Island. The presence of this eddy is thought to have a strong influence on nutrient loss on the surface. Our research shows that during the La Nina period, the eddies vorticity increased causing low surface chlorophyll in the surface the Banda Sea.