Apis mellifera subspecies exhibit strong adaptation to their respective natural habitats; however, they display varying responses to thermal stress. In the present study, we examined the expression of lethal(2)-essential-for-life-like (l(2)efl) gene variants (724449, 724231, 410087, 724405, 724488, 724274, and 724367), as well as histone-lysine N-methyltransferase trithorax (trx) and polycomb protein Su(z)12 mRNA, in the eggs of two honeybee subspecies that exhibit clear differences in their thermal adaptation. The results revealed significantly higher expression levels of (l2efl variants: 724449, 724231, 410087, 724405, 724488, 724274, and 724367), polycomb protein Su(z)12 mRNA (ID: 409170), and histone-lysine N-methyltransferase (trx) (ID: 408716) in the eggs exposed to thermal stress compared to untreated controls in both A. mellifera subspecies. The main fold change between treated and control eggs reached approximately 200-fold for l2efl-724367, 100-fold for l2efl-724274, 40-fold for l2efl-724488, suggesting a robust heat-shock-like mechanism in response to thermal stress in early embryos of both subspecies. The results also showed distinct changes in l2efl and trx expression levels in both subspecies. While A. m. carnica exhibited higher expression of certain l2efl variants and trx, A. m. jemenitica showed stronger activation of other l2efl members and Su(z)12. The expression of Su(z)12 increased 86-fold more in A. m. jemenitica than in A. m. carnica. This might reflect different adaptive strategies in both subspecies. These findings suggest that thermal exposure in A. mellifera embryos not only triggers classical stress-response genes but also modulates epigenetic pathways that could contribute to transgenerational thermotolerance.