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Abstract Among the natural ecosystems, forests and wetlands emit a sizable amount of carbon dioxide (CO2) and methane (CH4) through autotrophic and heterotrophic respiration and bacterial activities. Interestingly, some evidence suggests that a significant amount of CH4 is generated by the trees in forested ecosystems. The net ecosystem exchange (NEE), measured by the eddy covariance (EC) method, typically represents the net CO2 flux arising from the photosynthetic and respiration processes in the biosphere. This flux is subsequently partitioned into two components, the respired carbon and the assimilated carbon. However, the usual method of partitioning introduces significant errors in each of these fluxes. The present study was undertaken to address this issue where the NEE partitioning was constrained by using the carbon isotopic ratios of CO2. We used a real‐time in situ analyzer in a tropical forest in northeast India, the Kaziranga National Park. The greenhouse gas analyzer provided CO2 and CH4 concentrations, as well as their carbon isotopic ratios. The isotopic data were used to partition the EC‐derived NEE values and derive the isoflux values. Additionally, the isotopic data provided evidence of plant‐generated CH4 in conformity with some recent studies, which requires further investigation.