National target GHG emission reduction has been revised to 29 % below the Business as Usual (BAU) level by 2030. Indonesian government is preparing new Presidential Regulation about Low Carbon Development Initiative (LCDI) in replacing previous regulation for reducing GHG Emissions which called Rencana Nasional Penurunan Emisi Gas Rumah Kaca or RAN-GRK. The RAN GRK priority activities have concentrated in 5 sectors to reach the national target which are agriculture, forest and peatland, Energy and Transportation, Industry, and waste that have annual report for their potential emission reduction by activities from their area in each year. Indonesia has begun put coastal and marine sector into the national priority activities that have an influence on climate change, that is mangrove and seagrass which are Blue Carbon component. These ecosystems have higher carbon stocks per hectare compared to terrestrial forest. As report by Alongi et al. (2015) that Indonesian mangrove and seagrass was estimated in storing the 17 % of total carbon stock from global blue carbon ecosystem, having an annual potential emission at 0.029 Gt CO2-eq or equal to 3.2 % of emission from forest and peatland conversion (0.9 Gt CO2-eq) if mangrove and seagrass are