Abstract <p>The present study attempts to determine the contribution of repetitive DNA sequences to the formation of social structures in <i>Apis mellifera</i> honey bees. Despite progress in understanding the molecular basis of caste formation, particularly related to the Notch signaling pathway, the identification of genome-specific cis-regulatory elements remains incomplete. The present work focuses on characterizing the landscape of repetitive elements in the genomes of two honey bee subspecies, <i>A. m. mellifera</i> and <i>A. m. ligustica.</i> The study revealed that the increased copy number of mobile genetic elements in <i>A. m. ligustica</i> is a significant difference between the two subspecies. Furthermore, differentially expressed repetitive elements with the potential for cis-regulatory functions were identified. Concurrently, the analysis of the transcriptome showed minimal differences in the expression of mobile elements during caste differentiation, a fundamental process in the eusocial organization of bees. Furthermore, the analysis of transposon divergence between the subspecies indicated consistent changes in their repeat status correlating with time of origin. Taken together, the findings indicate a potential role of repetitive elements in the acquisition of new regulatory functions, which opens new perspectives for understanding the molecular mechanisms of honey bee social behavior.</p>