Photosynthesis and stomatal dynamics are the primary physiological processes directly affected by the concentration of CO₂ in the atmosphere and may determine a forest response to a scenario of elevated CO₂ (eCO2). CO₂-induced alterations in photosynthesis and stomatal behavior will likely lead to modified carbon allocation patterns as well as whole-tree water transport. Studies at the Duke Forest FACE site have shown a large increase in photosynthetic rates in loblolly pine trees growing under eCO₂ conditions relatively to those under ambient CO₂; stomatal conductance, on the other hand, was only slightly reduced under eCO₂ in periods of severe drought. Despite the vast amount of information available at the leaf-to-ecosystem levels, little is known about the molecular mechanisms controlling these changes and their effects on downstream metabolic processes. Within the context of a larger study using cDNA microarrays to evaluate the effects of eCO₂ on the expression of 1800 pine genes, we analyzed genes in the largest functional category present, “Carbon metabolism”, as well as genes related to hydraulic structure and function (cell wall related, aquaporins, and drought-responsive genes). No differential expression of genes coding for rbc_ss, accompanied by upregulation of several Rubisco chaperonin genes seems to corroborate the evidence of continued stimulation of photosynthesis under eCO₂. Upregulation of a thioredoxin-f-coding gene further emphasizes that interpretation. Several genes involved in carbon degradation are consistently upregulated under eCO₂. Not as many changes are observed in the water-transport related genes, although there are a few drought-induced genes, as well as some involved in cell wall formation, upregulated under eCO₂. These results will be discussed within the context of literature-based gas exchange values and our measures of hydraulic traits (wood anatomy and conductivity) in pine branches from the FACE site.