Understanding the molecular mechanisms underlying thermal acclimation and heat shock responses in marine ectotherms is critical for assessing their adaptive capacity in the context of climate change and climate extremes. This study examines the expression dynamics of heat shock proteins (HSPs) in the scallop Nodipecten subnodosus, shedding light on their role in thermal adaptation. Our analysis revealed the presence of several conserved functional signatures in N. subnodosus HSPs deduced amino acid sequences. Comparative gene expression profiling between two populations of N. subnodosus, maintained for 15 days under constant and oscillatory thermal regimes and then exposed to acute heat stress, revealed conserved adaptive traits. The heat-inducible nature of N. subnodosus HSP70 (HSPA8) gene expression highlights its potential as a stress marker, in contrast to its human homolog, which is constitutively expressed. Furthermore, the identification of HSP90 (HSPC3) and its overexpression during acute heat stress underscores its critical role in initiating a protective stress response. Population-specific responses in the magnitude of gene expression were observed; however, both populations exhibited similar overall patterns of HSP induction, suggesting a shared adaptive response mechanism. This study also elucidated the diversity and expansion of members of the HSP70 family members, specifically the HSPA12 subfamily, in N. subnodosus. This characteristic, previously observed in other bivalves, underscores the role of HSPA12 in environmental adaptation, providing molecular plasticity to withstand varying environmental pressures. These findings offer valuable insights into the molecular basis of thermal adaptation in N. subnodosus, highlighting the importance of HSPs in coping with environmental stochasticity under climate change scenarios.