Fluxes of CO2 froma green manuring crop,dhaincha(Sesbaniaaculeata) grown on a marginal (shallow basaltic) soil were quantified using the open path eddy covariance technique and the characteristics were related to various environmental parameters. Flux data was screened for various factors like wind from the tower, its frictional velocity, data monitored during rain events etc. and validated using the principle of energy balance closure. During the 82 days study period (9-August to 29-October, 2013), the net ecosystem exchange (NEE) averaged on a half-hourly basis ranged between +18.2 and - 43.1 ïmolm-2s -1.The maximum daytime capture occurred during 9-20 September when the crop was at its phase transfer from vegetative to flowering and abundant soil water was available. Daytime NEE was strongly controlled by soil moisture, soil temperature, net radiation and insolation.The dhaincha ecosystem had an average CO2 sink value of -1.52 ïmol m-2 s -1 as computed from the net daily exchange rates.