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Abstract Heat stress compromises wheat resistance to Hessian fly (HF, Mayetiola destructor (Say)) (Diptera: Cecidomyiidae) infestation. The objective of this research is to analyze the molecular basis of heat-induced loss of wheat resistance to HF infestation using RNA Sequencing (RNA-seq). To this end, two resistant wheat cultivars ‘Molly’ and ‘Caldwell’ containing the resistance genes H13 and H6, respectively, were infested with an avirulent HF biotype GP and treated with different temperatures to examine the impact of heat stress on their resistance phenotypes. Tissue samples collected from HF feeding sites in Molly plants were subjected to RNA-seq analysis to determine the effect of heat stress on transcript expression of genes in wheat plants. Our results indicate that resistance to HF infestation in Caldwell is more sensitive to heat stress than that in Molly, and that heat stress down-regulates most genes involved in primary metabolism and biosynthesis of lignin and cuticular wax, but up-regulate most or all genes involved in auxin and 12-oxo-phytodienoic acid (OPDA) signaling pathways. Our results and previous reports suggest that heat stress may impair the processes in wheat plants that produce and mobilize chemical resources needed for synthesizing defensive compounds, weaken cell wall and cuticle defense, decrease OPDA signaling, but increase auxin signaling, leading to the suppressed resistance and activation of susceptibility.