Juvenile Dungeness crabs must be able to tolerate a range of temperatures, as they inhabit the intertidal of bays of the west coast of North America. The aim of the study was to understand how gene expression in the heart changes throughout the molt cycle in response to temperature in juveniles from Bodega Harbor, CA. Two experimental set ups were used; the first grouped crabs into four molt stages: intermolt, early premolt, mid premolt, and late premolt, and exposed them to three acclimation temperatures (10°C, 15°C, and 20°C). In the second set of experiments intermolt crabs were exposed to either 15°C (ambient control) or 25°C for three days (sublethal). At the end of the incubation periods cardiac tissues were collected. mRNA expression of seven genes (AMPKα, RbS3, Rheb, NaKα, S6K, Akt, and mTOR) was determined using quantitative real-time PCR. For experiment one there were significant differences in gene expression for Rheb, NaKα, S6K, and Akt between temperature treatments. Also, there was a significant difference in Rheb and NaKα between molt stages. The second experiment did not yield any significant effects of three days at 25°C. Our data indicate that Rheb, NaKα, S6K, and Akt are markers for thermal acclimation and Rheb and NaKα are markers of molt stage. Supported by EU FP7 Marie Curie International Outgoing Fellowship PIOF-GA-2012-326483 to ACW, NSF grant IOS-1257732 to DLM.