Increasing seawater temperatures coupled with more intense and frequent heatwaves pose an increasing threat to marine species. In this study, the New Zealand green-lipped mussel, Perna canaliculus, was used to investigate the effect of genetics and ontogeny on thermal resilience. The culturally and economically significant mussel P. canaliculus (Gmelin, 1971) has been selectively-bred in New Zealand for two decades, making it a unique biological resource to investigate genetic interactions in a temperate bivalve species. Six selectively-bred full sibling families and four different ages, from early juveniles (6, 8, 10 weeks post-fertilisation) to sub-adults (52 weeks post-fertilisation), were used for experimentation. At each age, each family was exposed to a three-hour heat challenge, followed by recovery, and survival assessments. The shell lengths of live and dead juvenile mussels were also measured. Gill tissue samples from sub-adults were collected after the thermal challenge to quantify the 70 kDa heat shock protein gene (hsp70). Results showed that genetics, ontogeny and size influence thermal resilience in P. canaliculus, with LT50 values ranging between 31.3 and 34.4 °C for all studied families and ages. Juveniles showed greater thermotolerance compared to sub-adults, while the largest individuals within each family/age class tended to be more heat sensitive than their siblings. Sub-adults differentially upregulated hsp70 in a pattern that correlated with net family survival following heat challenge, reinforcing the perceived role of inducible HSP70 protein in molluscs. This study provides insights into the complex interactions of age and genotype in determining heat tolerance of a key mussel species. As marine temperatures increase, equally complex selection pressure responses may therefore occur. Future research should focus on transcriptomic and genomic approaches for key species such as P. canaliculus to further understand and predict the effect of genetic variation and ontogeny on their survival in the context of climate change.