Seagrass ecosystems are important carbon dioxide sinks that can sequester carbon for centuries as organic matter in sediment. They are also a major source of methane, a potent greenhouse gas, which limits their carbon sink capacity. However, data are lacking on their methane emission dynamics. Here, we conduct a one-year survey of carbon dioxide and methane concentrations and air-sea fluxes in Red Sea seagrass, mudflat, and coral backreef ecosystems. All ecosystems were sources of methane and carbon dioxide. Methane concentrations were lowest in the reef lagoon. We suggest that lagoons may be a globally important source of greenhouse gases. Methane concentrations were lower in seagrass than mudflat ecosystems at temperatures below 29.2 °C. Seagrass had the highest annual methane air-sea fluxes but the lowest global warming potential in carbon dioxide equivalent due to a decrease in its flux. Hence, seagrasses can help climate change mitigation compared to bare sediments.