Intraspecific hybridization has been a strategy used frequently in mollusc aquaculture to improve the performance of traits for productive interest. In this study, the effect of hybridization between a natural population (Arica = A) and a cultivated population (Coquimbo = C; without genetic management for more than 30 y) of the Peruvian scallop Argopecten purpuratus was evaluated to assess the effect of this strategy on the performance of the cultivated population in terms of growth, survival, and stress tolerance due to hypoxia and increased temperature. To this end, progenies from intrapopulation (C × C and A × A) and reciprocal hybrid (C × A and A × C) crosses were produced and were evaluated after 6 mo under sea cultivation and in a controlled environment. Stress responses were evaluated via metabolic rates and the transcriptional level of stress-associated genes [superoxide dismutase (SOD) and HSP70]. The results showed that CC and the reciprocal hybrids CA and AC had greater size and survival rates than AA; on the other hand, AA presented the highest metabolic rates when exposed to stress; and, in parallel, AA and both hybrids (CA and AC) presented greater antioxidant capacity (SOD) when exposed to hyperthermia. Therefore, growth and survival showed positive heterosis because the hybrids performed better in these traits than the parental mean. In addition, hybridization with the Arica population would allow the Coquimbo stock under cultivation to improve its resilience to temperature increases associated to oceanographic oscillations or to climate change.