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Qilian juniper (Sabina przewalskii Kom.) and Qinghai spruce (Picea crassifolia Kom.) represent different tree functional types, which can be found extensively in northwestern China. The former is drought-tolerant, whereas the latter is hygrophilous and shade-tolerant. We compared their intrinsic water-use efficiency (iWUE, inferred from carbon isotopic discrimination, delta>C-13, in their wood) as a function of atmospheric CO2 concentration, [CO2], and climate. delta C-13 of spruce was consistently a higher than that of juniper in semi-arid areas but was lower in arid areas. This difference was stable over time and demonstrated strong cross-correlations between species, although some subtle high-frequency (2 or 3 years) variations existed in both species, suggesting that regional climate may control carbon isotope discrimination. The < ratio (the [CO2] values in leaf intercellular and the atmosphere, respectively) of the juniper increased steadily over time, whereas that of the spruce showed a long-term downward trend. IWUE increased at all sites over the 150-year study period, mainly caused by increasing [CO2]. The relationship between iWUE and [CO2] reveals that the spruce was more sensitive than the juniper to increasing [CO2], suggesting a species-specific adaptation to long-term environmental changes. Correlations between the high-frequency variations in stable carbon discrimination (Delta) and climate indicate similar intra-site responses to climate in both species, but different response strengths. Overall, complex interactions of temperature and moisture on stable carbon discrimination during current growth seasons of both species were environmental-determined. Regulation of gas exchange and reduced transpiration may influence water and energy budgets directly; therefore species-dependent responses of trees to elevated CO2 should be considered in future research on global plant physiological ecology.