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Simple Summary: Upregulation of heat shock proteins (hsp) is a key mechanism to diminish heat stress in Apis mellifera. In this study, we investigated how histone methylation states present an epigenetic layer of hsp regulation in response to heat stress in two honeybee subspecies: A. m. jemenetica, a thermo-tolerant honeybee subspecies native to the Arabian Peninsula, and A. m. carnica, a subspecies occurring naturally in temperate regions of Central Europe. The results revealed significant changes in most histone methylation states of hsp investigated. The results also revealed higher variation in histone methylation states associated with hsp in A. m. carnica compared to A. m. jemenetica after exposure to moderately high temperature. This confirms that the response threshold is lower for A. m. carnica compared to A. m. jemenetica. We concluded that changes in histone methylation states play a key role in regulation of hsp in both A. mellifera subspecies. Genetic and epigenetic responses to environmental cues of worker honeybees mediate hsp synthesis, a key mechanism to tolerate high ambient temperatures in Apis mellifera. In this study, the chromatin immunoprecipitation assay followed by qPCR were used to determine alterations in histone methylation states (H3K27me2, H3K27me3, H3K4me2, and H3K4me3) associated with hsp/hsc/trx in A. m. jemenetica (thermo-tolerant subspecies) and A. m. carnica (thermo-susceptible subspecies) after heat treatment. The results revealed significant changes in enrichment folds of histone methylation states associated with hsp/hsc/trx. Indeed, the enrichment of H3K27me2 decreased strongly in response to heat stress. Changes in histone methylation states were significantly higher in A. m. carnica samples compared to A. m. jemenitica samples. Our study provides a new perception on linking histone post-translational methylation as an epigenetic mechanism of gene regulation with hsp/hsc/trx in A. mellifera subspecies exposed to heat stress. [ABSTRACT FROM AUTHOR]