Temperature is a critical environmental factor that affects all living organisms. Climate change is resulting in rising global temperatures with marine environments being especially vulnerable. My study aimed to elucidate the temperature-dependent molecular mechanisms deployed by five populations of N. vectensis along a naturally occurring thermal gradient along the Atlantic coast of the United States and Canada. Animals were exposed to one of three temperatures over a period of 30 days. Comparisons of transcriptome-wide gene expression indicated that there was not an overall conserved thermal stress response seen across populations or temperatures. Each population displayed unique gene expression profiles suggesting population-specific responses to temperature, even when the temperature differences were identical and the populations were geographically close in proximity. Unexpectedly, populations from the two most distant locations (Nova Scotia and South Carolina) shared more similarity in differentially expressed genes. Together the results from this study support a hypothesis that populations of this sea anemone have evolved largely unique temperature responses when cultured over long time periods. Future research comparing physiological and genomic differences between these locations will assist in understanding how the differences in DNA sequences may contribute to the transcriptional variation and how this variation impacts the ability to respond to broad temperature ranges.