Abstract This study investigated, using the closed chamber method, the impact of (1) vegetation community type (Typha latifolia, Cyperus papyrus and Phragmites mauritianus) in a natural tropical freshwater marsh wetland (marsh) and (2) conversion of a natural tropical freshwater marsh into a rice paddy wetland (rice paddy), on nitrous oxide (N2O) emission. Both the marsh and the rice paddy were continuously flooded, while the rice paddy was unfertilized. Average N2O emission from the marsh did not vary significantly (p > 0.05) among the vegetation communities, ranging from 0.5 to 0.6 μg m−2 h−1. Similarly, these N2O emission rates were not significantly different (p > 0.05) from those recorded in the rice paddy (0.7 ± 2.8 [SE] μg m−2 h−1). There was no significant correlation (p > 0.05) between environmental parameters and N2O emission. We concluded that vegetation community type does not affect N2O emission from natural tropical freshwater marshes under continuous flooding. Further, converting natural tropical freshwater marshes into continuously flooded and unfertilized rice paddies does not affect N2O emission but instead enhances carbon emission, as was depicted by the significantly lower (p > 0.05) soil organic carbon content in the rice paddy. In view of climate change mitigation, therefore, wetland management should give priority to the conservation/protection of natural wetlands.