Heat stress in plants hinders plant growth with important implications for crop yield as global surface temperatures are expected to rise throughout the 21st century. Boechera is a large genus in the family Brassicaceae and a close relative of model organism Arabidopsis thaliana. Boechera depauperata, a polyploid species native to the Sierra Nevada mountains of California, exhibits higher heat tolerance when compared to than other studied taxa in Boechera as well as the closely related model species Arabidopsis thaliana. Previous studies have determined that despite its increased thermotolerance, B. depauperata shows less upregulation of heat shock proteins when subjected to heat stress. This study uses transcriptomics in a two-pronged approach to discover other mechanisms providing B. depauperata its superior heat resistance. First, a transcriptome of B. depauperata was constructed de novo. Then, RNA-seq data from basal and acquired heat stress experiments in B. depauperata and A. thaliana were analyzed to identify differences in how each species responds to heat stress. Here I present findings suggesting three protective mechanisms active in B. depauperata which were not present or only weakly present in A. thaliana. In B. depauperata ubiquitins were upregulated, indicating a more robust autophagy response. In addition, chaperonin-60Beta2 was upregulated and this protein is known to form a protective complex with RuBisCO Activase (RCA) under heat stress. Boechera depauperata exhibited greater up- and down-regulation (fold change) of genes during heat stress. Gene ontology (GO) enrichment analysis showed GO terms known to protect plants from heat enriched at lower temperature in B. depauperata. GO analysis also showed more genes with unknown molecular function are enriched in B. depauperata under heat stress, suggesting novel mechanisms are involved in the heat shock response.