We measured carbon (C) stocks and fluxes and vegetation phenology in the world's oldest prairie restoration ( $ 65 years) and an adjacent prairie remnant in southern Wisconsin from 2001-2004 to quantify structural and functional differences. While the species distributions and frequency differed, the number of species measured per 1 m 2 quadrat were not significantly different (15.8 AE 4.4 and 14.1 AE 2.1 for remnant and planted [order for all reported values in abstract]; P 5 0.29), and the annual average aboveground net primary productivity (271 AE 51 and 330 AE 55 g C m À2 ) and peak leaf area index (2.9-4.9 m 2 m À2 ) were comparable under similar fire management. Total root biomass was not significantly different in 2002 (1736 AE 1062 and 1690 AE 459 g dry matter m À2 ) or 2003 (3029 AE 2081 and 2146 AE 898 g m À2 ), but annual average soil respiration (1229 AE 77 and 1428 AE 24 g C m À2 yr À1 ) was significantly higher in the restoration (Po0.0001). However, the prairie remnant contained 37% greater soil C (Po0.0001) in the top 25 cm. Soil respiration response to 10 cm soil temperature (Q 10 ) varied with respect to prairie and soil moisture conditions as annual Q 10 values ranged from 2.5 to 3.6. We calculated a range of net ecosystem production (NEP) values using estimated heterotrophic respiration and three root turnover values. Average NEP varied from À1.4 to 1.9 and À2.3 to 1.3 Mg C ha À1 yr À1 for the remnant and planted prairies, respectively. While these two prairies share similar structural components and functional attributes, the large uncertainty in NEP casts doubt as to whether we can verify these prairies as C sources or sinks without direct measures of heterotrophic respiration and root turnover. We argue that quantitative studies of C exchange in prairies, which differ in restoration methodology, management intensity, and fire frequency, are needed to solidify the relationship between prairie structure and potentially desired functions such as C sequestration.