Although oysters are exposed to seasonal temperature changes, they are frequently subjected to acute temperature stress during emersion due to their attachment on their rocky shore habitats. To understand the effect of acute temperature elevation on the whole transcriptome of susceptible Pacific oyster Crassostrea gigas over time, the oysters were exposed to temperatures ranging from the control 20°C to 32°C for 72 h. We compared the genome-wide patterns of mRNA expression of susceptible oysters with those obtained from thermotolerant oysters. RNA-seq identified differentially expressed stress responsive Gene Ontology (GO) terms and relevant transcripts following acute thermal stress. The clearest pattern between susceptible and tolerant oysters was the dramatic differences in transcriptional expression in the hsp70 gene family. GO terms and genes typically associated with oxygen binding were also repressed compared to those of tolerant oysters. This study provides insights into the significant differences in molecular response of susceptible C. gigas to acute heat stress, and the will further our understanding of the basis of molecular adaptation in the Pacific oyster.