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Heat stress has become a major threat to crop production due to global warming; however, the mechanisms underlying plant high-temperature sensing are not well known. In plants, the membrane-anchored receptor-like kinases (RLKs) relay environmental signals into the cytoplasm. In a previous study, we isolated a wall-associated RLK-like (WAKL) gene CaWAKL20 from pepper (Capsicum annuum L.). Here, the amino acid sequence of CaWAKL20 was characterized and found to consist of conserved domains of WAK/WAKL family, including an extracellular region containing a GUB-WAK binding domain and a degenerated EGF2-like domain; a transmembrane region; and an intercellular region with an STKc catalytic domain. Moreover, CaWAKL20 transcription was inhibited by heat stress, whereas it was induced by both ABA and H2O2 treatments. Silencing of CaWAKL20 enhanced pepper thermotolerance, while overexpression decreased Arabidopsis thermotolerance. Additionally, Arabidopsis lines overexpressing CaWAKL20 showed less sensitivity to ABA during seed germination and root growth. Finally, the survival rate of Arabidopsis seedlings under heat stress treatment was enhanced by ABA pre-treatment, while it was compromised by the overexpression of CaWAKL20. Furthermore, the heat-induced expression of several ABA-responsive genes and some key regulator genes for thermotolerance was decreased in Arabidopsis CaWAKL20-overexpression lines. These results suggest that CaWAKL20 negatively modulates plant thermotolerance by reducing the expression of ABA-responsive genes, laying a foundation for further investigation into the functional mechanisms of WAKs/WAKLs in plants undergoing environmental stresses.