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Food production including fisheries production is responsible for a quarter of global anthropogenic (GHG) greenhouse gas emissions. Greenhouse gas emissions from marine capture fisheries are generally not specifically accounted for in the calculation of global greenhouse gas emissions, and are often generalized as part of other sectors such as energy. We carried out a quantitative quantification of data on fuel consumption of capture fishing fleets in the coastal areas of West Java Province in 2007-2016. The data is then converted to CO2 emissions which are then compared with the potential of CO2 uptake by coastal ecosystems (i.e. mangrove and seagrass) in West Java Province. We estimate that capture fisheries in West Java Province consume about 60,944.55 kilolitres of fuel in 2016 and produce a total 1,353 million tons of CO2 (0.2% of total West Java CO2 emissions in 2016). CO2 emissions from the capture fisheries industry increased by 34.35% between 2007 and 2014, which was in line with the increase in fisheries production in that year. The increase in emissions was driven mainly by the increase in the number of fishing vessels with size of less than 30 GT. The geographical characteristics of coastal waters in the north and south of West Java also influence the number of fishing fleets and CO2 sequestration by coastal ecosystems. The increase in fishing fleets is also thought to have a real positive correlation with fisheries subsidy policies for fishermen. Building a strategy for effective and efficient capture fisheries activities is expected to be able to divert existing incentives to increase or maintain an ecosystem conservation area that absorbs CO2 emissions.