Various sources emit greenhouse gases such as CO and CH. Among the natural ecosystems, forests and wetlands emit a sizeable amount of these gases by means of autotrophic, heterotrophic respiration and bacterial activities. Additionally, a relatively new source has been detected; the emission of CH by trees and plants. Growing evidence suggests that a significant amount of CH is generated by the trees in forested ecosystems. The net ecosystem exchange (NEE), measured by an eddy covariance (EC) system, typically represents the net CO fluxes arising due to the biosphere’s photosynthetic and respirative processes. The net flux derived by this system is subsequently partitioned into two components, the respired carbon, and the assimilated carbon. However, the partitioning processes may have their shortcomings, which introduce significant errors. To reduce the uncertainty, the NEE has been constrained by measuring the isotopic values of the GHGs using a real-time analyzer in a tropical forest of north-east India, the Kaziranga National Park. The GHG analyzer provided CO and CH concentrations, as well as their carbon isotopic ratios. The isotopic data were used to partition the EC derived NEE records, which showed a good agreement with the EC measurements within the limits of experimental uncertainty. However, long-term observation is required to establish the potential of this relatively new method in this endeavor. Additionally, the isotopic data provided strong evidence of plant generated CH, which was apparently not possible to identify by the conventional means.