Wetlands are the largest natural source of the greenhouse gas methane to the atmosphere. Despite the fact that a large percentage of wetlands occur in tropical latitudes, methane emissions from natural tropical wetlands have not been extensively studied. The objective this research was to compare methane emissions from three natural tropical wetlands located in different climatic and ecological areas of Costa Rica. Each wetland was within a distinct ecosystem: (1) a humid flow-through wetland slough with high mean annual temperatures (25.9 °C) and precipitation (3700 mm yr−1); (2) a stagnant rainforest wetland with high mean annual temperatures (24.9 °C) and precipitation (4400 mm yr−1); or (3) a seasonally wet riverine wetland with very high mean annual temperatures (28.2 °C) and lower mean annual precipitation (1800 mm yr−1). Methane emission rates were measured from sequential gas samples using nonsteady state plastic chambers during six sampling periods over a 29-month period from 2006 to 2009. Methane emissions were higher than most rates previously reported for tropical wetlands with means (medians) of 91 (52), 601 (79), and 719 (257) mg CH4-C m−2 day−1 for the three sites, with highest rates seen at the seasonally flooded wetland site. Methane emissions were statistically higher at the seasonally wet site than at the humid sites (P<0.001). Highest methane emissions occurred when surface water levels were between 30 and 50 cm. The interaction of soil temperature, water depth, and seasonal flooding most likely affected methanogenesis in these tropical sites. We estimate that Costa Rican wetlands produce about 0.80 Tg yr−1 of methane, or approximately 0.6% of global tropical wetland emissions. Elevated methane emissions at the seasonally wet/warmer wetland site suggest that some current humid tropical freshwater wetlands of Central America could emit more methane if temperatures increase and precipitation becomes more seasonal with climate change.