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The Eastern of Indonesian Sea waters as a part of Indonesian Sea Large Marine Ecosystem accomodates the Tropical Ocean Productivity. Those regions also have an important sites for Indonesian fisheries. As a part of the Tropical Ocean Productivity contains of chlorophyll-a and Carbon Organic concentrations. The amount of organic carbon manufactured by primay producers through a photosynthesis process. However, the primary producers immediately respire some of the organic carbon for their own energy, so the rest organic carbon that is available as food for the higher trophic levels called Net Primary Productivity (NPP). The aim of this study was to investigate the current profiles of chlorophyll-a and carbon organic from Net Primary Productivity concentrations based on in-situ measurement. We measured chlorophyll-a and organic carbon concentrationsat surface layer or in the euphotic zone on a cruise carried in 2017 at Banda, Maluku and Sulawesi Seas.The study reveals that the range of chlorophyll-a and organic carbon concentration were 0.1 – 0.75 mg/m3 and -0.076 – 0.338 mg C/m3/d in Banda Sea. The higher chlorophyll and organic carbon concentrations found in Maluku dan Sulawesi Seas with the range value were 0.4441 – 1.137 mg/m3 and -0.680 – 8.789 mg C/m3/d. These study results indicate that there was general relationship between chlorophyll a concentrations and organic carbon from Net Primary Productivity in the euphotic layers.This study suggests that the water fertility assosiated with chlorophyll a in Maluku and Sulawesi Seas are categorized as mesotrophic water and oligotrophic water for Banda Sea.