Mangrove ecosystem is among the most richest carbon in the tropics . The study by Donato, et.al (2011) estimated the carbon density of about 1.028 Tg (1 Tg = 1,000 Mg) per hectare. It was also estimated that mangrove deforestation resulted in emissions of 0.02 and 0.12 Pg carbon per year, which contributes to 10% of global deforestation. Study on mangrove mapping and estimation of carbon stocks and emissions over this particular ecosystem especially in the tropical regions is essential, as this ecosystem is under serious threats, highly degraded and deforested to other land uses. Over the past 50 years the area of mangrove forests has sharply declined by 30-50% due to coastal development, aquaculture and over-harvesting (Murdiyarso et al. 2012). Mapping of above ground biomass (AGB) on mangrove ecosystem in the tropics is important, since it may reduce uncertainty in carbon accounting over this ecosystem and to support climate change initiatives to decide on benefits distribution following carbon emissions reduction . This study employs integration of Lidar and Landsat data combined with in-situ measurement to assess and calibrate global above ground biomass estimate (Baccini et al. 2012). The study objectives are to: 1) estimate the extent of carbon stocks over mangrove ecosystem in the tropics combining spatial and in-situ data, and 2) to find possibilities for more accurate biomass mapping over this particular ecosystem.