Abstract: Global warming may drive adaptive evolution by influencing natural selection and utilizing temperature-related phenotypic plasticity. However, predicting the evolutionary patterns of phenotypic plasticity under climate change remains a challenge, underscoring the need to elaborate on the underlying genetic and molecular mechanisms. In this study, we focus on the expression plasticity divergence of heat shock protein 90 (Hsp90), which is temperature responsive and exhibits a strong selective sweep in the upstream noncoding region of two allopatric congeneric oyster species: cold-adapted Crassostrea gigas and warm-adapted Crassostrea angulata. Functional characterization confirmed Hsp90 expression as an ideal proxy for thermotolerance. The evolutionary divergence in constitutive and plastic expression patterns represents adaptation to the mean and variance in habitat temperature, respectively. By combining forward and reverse genetic approaches, four causative loci with G + G × E effects were identified in the Hsp90 promoter regions of C. gigas and C. angulata, indicating cis-variations. Moreover, the g.-2291G allele of the causative locus in C. angulata is specifically bound to by the positive transcription factor purine-rich element binding protein B (PURB), explaining the constitutive expression of Hsp90. Meanwhile, the response of PURB to thermal stress determines the magnitude of plastic Hsp90 expression in C. angulata. This integrative study revealed that cis-variations interact with trans-variations and underlie the G × E effect under environmental changes, thereby mediating the divergence in plastic gene expression. Furthermore, we established a paradigm for studying genetic variants and their G × E impacts at a finer resolution, i.e., single-nucleotide level, in nonmodel organisms. The findings may deepen our understanding of the significant role of phenotypic plasticity in modulating adaptive responses and promote predictions of adaptive potential in marine organisms under climate change.