The biogeographic distribution of organisms is determined by physiological characteristics that enable a population to persist in a specific location. Global climate change effects are anticipated to increase the physiological stress experienced by organisms. Consequently, it is important to understand physiological responses to environmental stress and the mechanisms used by animals to cope with variable conditions. I investigated the physiological response to environmental stress in two species of mussel from New Zealand, Perna canaliculus and Mytilus galloprovincialis, using quantitative PCR and ecological field experiments. A series of laboratory and field experiments were done to manipulate stress levels and the expression levels of three heat shock protein genes (hsp24, hsp70, hsp90) were measured. A transcription regulatory gene (elf2) and a cell cycle regulatory gene (tis11d) were also measured. The dynamics of stress response gene expression in response to acute stress and gene expression changes in the natural population due to varying forms of environmental stress were tested. Between-zone translocations of different sized M. galloprovincialis and P. canaliculus were done at two sites in both east and west regions of the South Island of New Zealand. Site was found to be the most important factor in stress response. Apparent low food and high exposure stress interacted to create the particularly elevated stress response at the Timaru site. The adaptive ability of mussels transplanted between sites with varying environmental conditions was also tested. Results suggest that acclimation may be limited under stressful conditions. Furthermore, I found that P. canaliculus, the predominantly low-zone species, had a lower stress response than M. galloprovincialis, which was contradictory to predictions. The investigations described in this thesis suggest that interactive effects of abiotic stress and food limitations are particularly challenging for animals. With the severity of climate change scenarios predicted, changes in water quality and aerial and seawater temperature suggest mussel populations are likely to be negatively affected in the future. This work also illustrates the great potential to utilise molecular techniques for analysis of physiological processes of non-model organisms in a real-world setting.