The study of the microbiome of the mite Varroa destructor is crucial for understanding parasite-host interactions and their potential health implications for honey bees (Apis mellifera). The aim of this research was to characterize the microbial diversity of Varroa destructor populations collected from the body surface of honey bees and compare it with microbiome of Apis mellifera. DNA isolation was performed using standard methods, followed by next-generation sequencing (NGS) of the V3-V4 region of the 16S rRNA gene. The obtained bioinformatic data underwent taxonomic analysis, enabling the identification of dominant bacterial genera present in the Varroa and Apis mellifera microbiome. Results revealed significant microbial diversity, with dominance primarily by bacteria belonging to the families Acetobacteraceae, Morganellaceae, and Segniliparaceae. The identified bacteria may play a critical role in the pathogenicity of Varroa destructor, directly or indirectly affecting the health and condition of bees. These findings provide new insights into potential therapeutic and preventive targets for protecting bee colonies against the detrimental effects of Varroa mites.