Patients with atopic dermatitis often have an altered microbiota with decreased microbial diversity and increased colonization of Staphylococcus aureus (S. aureus), especially in lesional skin. Whether this dysbiosis is a cause or consequence of atopic dermatitis is still unclear. However, it is known that atopic skin is characterized by increased transepidermal water loss and decreased pH, both indicators of impaired skin barrier function. This defective skin barrier is also associated with lower level of antimicrobial peptides, which further facilitates the colonization and entry of pathogens. Atopic dermatitis most often develops during infancy, when the immune system is still maturing, and early skin microbial colonization and establishment can influence this immune maturation. As the microbiome can be influenced by a number of both endogenous and exogenous factors, it has been hypothesised that variations in the microbial community of the skin during infancy could impact the development of atopic disease. Therapy targeting the gut microbiome through probiotics has been widely studied, but with different approaches and varying results. Directly targeting the skin microbiota is less studied but shows promising results with decreased colonization of S. aureus and improvement of the severity. In this chapter we review the available literature on what is known about the skin microbiota in atopic dermatitis patients. We will cover the development of the skin microbiota and its influence on the immune system, the characteristics of atopic skin microbiota and how it is affected by treatment, as well as discuss potential therapies targeting the gut and skin microbiome in atopic dermatitis treatment and prevention.