Estuaries are characterized by extreme fluctuations in CO(2) levels due to bouts of CO(2) production by the resident biota that exceed its capacity of CO(2) consumption and/or the rates of gas exchange with the atmosphere and open ocean waters. Elevated partial pressures of CO(2) (P(CO(2)); i.e. environmental hypercapnia) decrease the pH of estuarine waters and, ultimately, extracellular and intracellular pH levels of estuarine organisms such as mollusks that have limited capacity for pH regulation. We analyzed proteomic changes associated with exposure to elevated P(CO(2)) in the mantle tissue of eastern oysters (Crassostrea virginica) after 2 weeks of exposure to control (∼39 Pa P(CO(2))) and hypercapnic (∼357 Pa P(CO(2))) conditions using two-dimensional gel electrophoresis and tandem mass spectrometry. Exposure to high P(CO(2)) resulted in a significant proteome shift in the mantle tissue, with 12% of proteins (54 out of 456) differentially expressed under the high P(CO(2)) compared with control conditions. Of the 54 differentially expressed proteins, we were able to identify 17. Among the identified proteins, two main functional categories were upregulated in response to hypercapnia: those associated with the cytoskeleton (e.g. several actin isoforms) and those associated with oxidative stress (e.g. superoxide dismutase and several peroxiredoxins as well as the thioredoxin-related nucleoredoxin). This indicates that exposure to high P(CO(2)) (∼357 Pa) induces oxidative stress and suggests that the cytoskeleton is a major target of oxidative stress. We discuss how elevated CO(2) levels may cause oxidative stress by increasing the production of reactive oxygen species (ROS) either indirectly by lowering organismal pH, which may enhance the Fenton reaction, and/or directly by CO(2) interacting with other ROS to form more free radicals. Although estuarine species are already exposed to higher and more variable levels of CO(2) than other marine species, climate change may further increase the extremes and thereby cause greater levels of oxidative stress.