The green-lipped mussel (Perna canaliculus Gmelin, 1791) is an economically and ecologically important marine species within New Zealand, yet the ability of adult mussels to cope with acute temperature change remains unknown. To address this, we sought to characterize the thermotolerance capacity of P. canaliculus adults and, using metabolomics, identify any metabolic biomarkers of thermal stress in this species. To achieve this, mussels were exposed to a 3 h acute temperature challenge using temperatures of 20 °C (Ambient), 25 °C, 29 °C, 31 °C, 33 °C, and 35 °C. No mortality was observed in mussels exposed to 31 °C or less, even after 30 days recovery. However, mussels exposed to 33 and 35 °C exhibited 100% mortality within 48 h of the challenge. Gill tissues were harvested from mussels for metabolomic analysis of thermal stress biomarkers via Gas Chromatography-Mass Spectrometry (GC-MS). Discriminant Function Analysis (DFA) of 52 metabolites identified eight key biomarkers indicative of thermal stress in this species (i.e., cis-11-Eicosenoic acid, Palmitic acid, Proline, GABA, Aspartic acid, Fumaric acid, beta-Alanine and Asparagine). These metabolites were entirely consistent in their ability to classify the exposure temperature that mussels experienced, indicating that the discriminatory capacity of these biomarkers was strong. Therefore, our results reveal that mortality in thermally-stressed adult P. canaliculus seems assured once temperatures reach 33 °C. Additionally, metabolite biomarkers can discriminate those mussels exhibiting varying levels of thermal stress; thus, metabolomics offers a new tool for physiologists seeking to gain greater mechanistic understanding of the effects of acute thermal stresses on invertebrate species.