Availability of nitrogen (N) is a critical factor determining plant responses to high CO2. Elevated CO2 affects N metabolism, depending on the nitrogen source. However limited information is available on how various forms of N affects morphology and metabolism of plant under elevated CO2. Similarly elevated CO2 induces changes in stomatal and epidermal parameters in plants. Different N forms had profound effects on morphology both under ambient CO2 and elevated CO2. The negative effects of ammonium nutrition were manifested as reduction in root length, root surface area, chlorophyll a:b ratio, and thinner leaves, in elevated CO2 also. When ammonium nutrition was supplemented with nitrate ions, enhancement of various morphological, biochemical and anatomical parameters was more in ECO2 than when only nitrate was given. Hence supplimenting nitrate nutrition with ammonium ions might be beneficial for wheat under elevated CO2 conditions in future.