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Changes in vegetation structure and composition, particularly due to the invasion of exotic species, are predicted to influence biosphere-atmosphere exchanges of mass and energy. Invasion of Cynara cardunculus (cardoon or artichoke thistle), a perennial, non-native thistle in coastal California grasslands presently dominated by non-native annual grasses, may alter rates of ecosystem CO(2) exchange and evapotranspiration (ET). During spring and summer 2006, we compared midday maximum net ecosystem CO(2) exchange (NEE) and ET among adjacent grassland plots where Cynara was present and where it was absent. Measurements of NEE supported the prediction that deeply-rooted Cynara increase midday ecosystem C-assimilation. Cynara-mediated shifts in NEE were associated with increases in ecosystem photosynthesis rather than changes in ecosystem respiration. Furthermore, the presence of Cynara was associated with increased ET during the growing season. An increase in aboveground live biomass (a proxy for leaf area) associated with Cynara invasion may underlie shifts in ecosystem CO(2) and water vapor exchange. Following mid-growing season sampling during April, we removed Cynara from half of the Cynara-containing plots with spot applications of herbicide. Three weeks later, midday fluxes in removal plots were indistinguishable from those in plots where Cynara was never present suggesting a lack of biogeochemical legacy effects. Similar to woody-encroachment in some semi-arid ecosystems, Cynara invasion increases midday ecosystem CO(2) assimilation and evapotranspiration rates and has the potential to increase C-storage in California coastal grasslands.