The Akoya pearl oyster is an economically important species farmed throughout Japan and China, and on a small scale in Australia. Recent proliferation of Akoya viral disease (AVD) has dramatically reduced both wild and farmed populations in Asia. It is thought that AVD is exacerbated by anthropogenic pressures associated with over-crowding and stress caused by fluctuations in the environment, as well as by husbandry and handling. To test the effects of these stressors, the differential expression of genes encoding three antioxidant enzymes (peroxiredoxin, PRx; glutathione-S-transferase, GST; glutathione peroxidase, GPx) and the generic stress biomarker heat shock protein 70 (HSP-70) was investigated using quantitative real-time PCR on mRNA extracted from gill tissues of Pinctada fucata that had been exposed to either mechanical agitation (MA, a combination of air exposure and shaking) or air alone for 1. h and 6. h. We observed a significant decline (up to 50%; p < 0.05) in the expression of both GST and PRx 60. min after oysters were exposed to air and MA. GPx transcription declined significantly 60. min after exposure to MA. Hierarchical cluster analysis and multidimensional scaling (MDS) demonstrated that, even though no significant differences were identified in the expression of these genes 6. h after exposure to stress, there was still a clear differentiation between controls and the two stress treatments. After 6. h, the MDS analysis showed that antioxidant enzyme expression was intermediate between the 60. min time point and the non-stressed controls. The MDS plot also demonstrated that there was no clear distinction between exposure to air and MA, suggesting that air exposure (which was a component of both treatments) is the main causative agent of transcriptional stress responses. HSP-70 expression also declined when oysters were exposed to both stressors, but these decreases were not statistically significant. Overall, the data suggest that the antioxidant systems of oysters are affected by exposure to air. This contributes to a growing understanding of short-term stress responses in bivalve molluscs and their potential effects on cellular homeostasis.