The global community is struggling with mitigating the effects of widespread habitat loss and degradation; the effects of which are being further magnified in the face of global climate change. Quality natural habitat is becoming increasingly limited and atmospheric carbon levels continue to rise. Therefore, land managers responsible for multiuse management are often faced with the dilemma of managing ecosystems for biodiversity, as well as optimizing ecosystem services such as carbon storage and sequestration. However, some management techniques used to meet these objectives may yield conflicting results, specifically, the management tool of prescribed fire. Fire is crucial in maintaining species composition and structure in many ecosystems, but also results in high carbon emissions. Thus, it is important for land mangers to achieve the most efficient prescribed fire management regime to both preserve plant and animal communities, and optimize carbon storage. A former ranchland at the Disney Wilderness Preserve, Central Florida, USA is being restored to native ecosystems and managed to preserve biodiversity and increase carbon storage. This study quantified the carbon stocks within the aboveground biomass, litter, and top 90 cm of soil in five ecosystems at the Disney Wilderness Preserve, all of which are managed with prescribed fire every two to three years. These carbon stocks were compared in ecosystems in different stages of restoration: bahia grass pasture, pasture in restoration for longleaf pine flatwoods, and restored longleaf pine flatwoods. The carbon stocks were also compared among three restored flatwoods communities: longleaf pine flatwoods, slash pine flatwoods, and scrubby flatwoods. To determine the effects of the current prescribed fire management, carbon stocks were quantified and compared in recently burned areas (burned 4 months prior) and areas burned two to three years prior, in all ecosystems. Soil carbon properties were assessed using ¹³C isotope analysis. Aboveground biomass and litter carbon stocks were found to increase with higher stage of restoration, and were significantly less in areas with recent fire management. The results of this study did not provide evidence that soil carbon stock was significantly different in different stages of restoration or at different times since fire, but soil carbon stock was found to be significantly different among the flatwoods communities. In un-restored pasture and pasture in restoration sites, the soil was found to be increasingly depleted in ¹³C with increasing soil depth. This pattern indicated that carbon in the upper, more labile soil carbon pool had been derived from current C4 pasture or native grasses, while carbon in the deeper, more stable carbon pool is a legacy of the historical C3 forest vegetation that existed prior to conversion to pasture. Additionally, a pattern of less depletion in ¹³C with increasing time since deforestation was noted, indicating an increasing loss of historic forest carbon with increasing pasture age. As the pastures in restoration for longleaf pine flatwoods mature, the isotopic composition of the soil profile in the restored longleaf pine flatwoods may serve as a reference value for the soil profiles of these sites. Overall, the mean carbon stock in the aboveground biomass, litter and top 90 cm of soil in the un-restored pasture was ~13.3 kg C/m², the carbon stock in the pasture in restoration was ~12.7 kg C/m², the longleaf pine flatwoods had the highest carbon stock at ~17.7 kg C/m², the scrubby flatwoods had the smallest carbon stock at ~7.7 kg C/m², and the slash pine flatwoods had a carbon stock of ~15.8 kg C/m².