The atmospheric methane (CH4) concentration has increased in recent years due to natural and anthropogenic causes. Hence, it is essential to quantify the potential sources of CH4 to understand the factors responsible for its fluxes on a local to regional scale through in situ observations. Coastal wetlands, particularly the mangrove ecosystems in the tropical and subtropical coasts, are significant sources of CH4. In this study, we used an eddy covariance-based technique to measure the CH4 fluxes in a mangrove ecosystem in Pichavaram, South India. The daily mean CH4 flux ranged from 12 to 26 nmol m−2 s−1 during the wet season and from 6 to 20 nmol m–2 s–1 during the dry season. The monthly mean flux during the wet period was between 0.8 and 1.8 g CH4 m−2 month−1, and in the dry season, it was between 0.4 and 0.6 g CH4 m−2 month−1. The visual correlogram and structural equation modelling technique revealed that air temperature, creek water dissolved oxygen, soil organic carbon, and redox potential are important factors that control the CH4 fluxes. The results suggest that the Pichavaram mangrove wetland acts as a source for CH4. Our results also indicate that tidal inundation and seasonal variations in atmospheric temperature and water salinity are key factors affecting the CH4 flux in the Pichavaram mangrove ecosystem.