In New Zealand there is an inclination to use local, native species for ecotoxic hazard assessments rather than internationally recognized, standard species for the characterization of environmental hazards. This includes using species with cultural relevance and those of commercial value, for example the NZ green-lipped mussel, Perna canaliculus. Due to New Zealand historically having low levels of contamination relative to the rest of the world sublethal endpoints, or biomarkers, may be necessary to predict potential environmental impact before it occurs. Although the internationally recognized mussel, Mytilus galloprovincialis, coexists across New Zealand, P. canaliculus, has a broader ecological niche and is capable of thriving in soft sediment, which may lead to exposure to sediment bound contaminants that M. galloprovincialis may not interact with. The specific aim of this research was to develop and validate RT-qPCR primers for P. canaliculus, targeting a suite of genes for various mechanistic responses (oxidative stress, xenobiotic transfer, membrane transportation, cellular and DNA response/repair, and endocrine disruption). P. canaliculus was exposed to two reference contaminants, benzo[α]pyrene and copper, that are well studied and well known to induce sublethal responses in M. galloprovincialis. The results of the present study found modulation of oxidative stress, xenobiotic transfer, and genotoxicity genes which is consistent with previous results reported for other mussel species, demonstrating P. canaliculus could potentially be used as an indicator species for environmental risk assessment of ecotoxicological hazard assessments. We also found that membrane transport genes were modulated after exposure to both copper and benzo[α]pyrene, suggesting that these chemicals may have other mechanisms of toxicity that have not been fully investigated. This study developed 11 novel biomarkers for P. canaliculus and is the first experiment to implement gene expression for P. canacliculus in an ecotoxicological context.