The pallid sturgeon (Scaphirhynchus albus) is a federally endangered species, endemic to the Mississippi River drainage, stretching from the upper Missouri River in Montana to the Mississippi River, and continuing to the Gulf of Mexico. They are largely sympatric throughout this range with a close congener, the shovelnose sturgeon (S. platorhynchus), although speciation may have occurred when they were isolated in different refugia. In this study, we examined gene expression differences among pallid and shovelnose sturgeon families in response to heat stress. Gene expression can be considered a phenotype, and therefore, variability in expression can have an adaptive role in species. Additionally, we compared our results to a previous expression study that utilized RNA-Seq. We developed viable primer pairs for five genes in order to conduct RT-qPCR assays. There were significant differences in heat stress response between pallid and shovelnose sturgeon, potentially indicative of different evolved stress response pathways. Our species results contrasted with results from the previous study, indicating that further research is needed to improve the robustness of the results. Additionally, we found that offspring of hatchery and wild pallid sturgeon demonstrate different responses to heat stress, and potentially general stress that can occur in a hatchery environment. Overall, this study lays the groundwork for future research that can incorporate a larger suite of families to improve the robustness necessary to make actionable management recommendations.