This study tested the proteomic responses of three spatially distinct Sydney rock oyster populations to elevated pCO2. Oysters were collected from environmentally different sites, two chronically affected by acid sulfate soil. Oysters from each of the three populations were exposed to ambient (380μatm) or elevated (856 and 1500μatm) pCO2 for 4 weeks. Subsequent proteomic analysis from haemolymph revealed that (1) there were differences between the proteomes of the three populations after exposure to ambient pCO2, and (2) the different oyster populations mounted significantly different responses to elevated pCO2. Proteins that differed significantly in concentration between pCO2 treatments fell into five broad functional categories: energy metabolism, cellular stress responses, the cytoskeleton, protein synthesis and the extracellular matrix. This is consistent with the hypothesis that environmental stress in oysters leads to a generic response involving increased mitochondrial energy production to maintain cellular homeostasis. Proteins involved in the cytoskeleton and energy metabolism were the most differentially expressed and were seen in all three oyster populations. Differences between populations in their proteomic responses suggested that the local environments from which oysters originate may affect their capacity to respond to ocean acidification.