This study aimed to analyze the flux of CH4 gas in the sediments of mangrove and seagrass ecosystems in Tanjung Tiram, Ambon Bay. The research was conducted in May – June 2024. The mangrove and seagrass ecosystems at this location get inputs from the organic matter originating from litter production and domestic waste from people living around the ecosystem area. In each ecosystem, three observation points were determined based on the sediment type: sand, muddy sand, and sandy mud, each coded M1, M2, and M3 for mangrove and L1, L2, and L3 for seagrass ecosystems. Gas sampling was carried out by placing cylinder covers on each sediment type. Furthermore, 10ml of gas was taken seven times with an interval of 30s, namely 0, 30, 60, 90, 120, 150, and 180s. The gas was put into a vial, and then the gas concentration was analyzed using chromatography (GC-MS), flux, and global warming potential. The single factor ANOVA and t-test (α = 0.05) were carried out to determine the difference in each sediment's average gas concentration. The results showed that the average comparison of CH4 gas concentrations in mangrove and seagrass ecosystems (M:L) showed no significant difference with P = 0.0637 (P> 0.05). The average CH4 flux in mangrove sediments was 0.1476mg/ m2/ hour, more significant than that in seagrass sediments, which was 0.1424mg/ m2/ hour. M1 and L1 recorded the most significant CH4 fluxes in each ecosystem sediment, which were 0.1794 and 0.1509mg/ m2/ hour. Meanwhile, the most minor flux was found in M2, which was 0.1005mg/ m2/ hour, and L3, which was 0.1320mg/ m2/ hour. The GWP of mangrove sediments was 3.6907mg CO2e /m2/ hour, more significant than the seagrass GWP of 3.5590mg CO2e/ m2/ hour. The flux of CH4 gas was significantly affected by the sediment type, especially in sandy sediments. It is related to the level of porosity of sediment, which acts as a circulating space for methane gas produced from the degradation process of organic matter contained in each type of sediment. The flux and GWP values of methane gas released from sediments of mangrove and seagrass ecosystems should not be ignored in climate change mitigation, especially in areas with very low-density levels and high organic waste inputs.