The skin microbiota is a complex ecosystem consisting of bacteria, fungi and viruses. The role of the human skin microbiota is to maintain homeostasis in the body. Disruption of the balance of the natural composition of the human microbiome can lead to the development of inflammation and infection. Atopic dermatitis is a chronic and recurrent non-infectious, inflammatory dermatosis characterised by erythematous and exfoliative skin lesions, accompanied by pruritus and a tendency to superinfection. Defect in the epidermal barrier, immune dysfunction and changes in the composition of the skin microbiome underlie the pathogenesis of atopic dermatitis. It has been found that the diversity of atopic skin microbiota is significantly reduced, with a decrease in the number of Cutibacterium, Streptococcus, Acinetobacter, Corynebacterium and Prevotella, and a concomitant increase in the percentage of Staphylococcus bacteria, especially S. aureus. It accounts for about 20% of skin microbiome in healthy people, while in patients with atopic dermatitis the percentage of S. aureus can increase up to 30–100%. In addition, there is a positive correlation between S. aureus skin colonisation and disease severity. S. aureus plays a key role in the development of skin inflammation in the course of atopic dermatitis, including through the induction of lymphocyte expansion, release of cytokines, pro-inflammatory lipoproteins, and stimulation of mast cell degranulation. Therefore, properly selected and regular treatment of atopic dermatitis diversifies the skin microflora, often leading to clinical improvement in the patient.