Skin microbiota is a complex ecosystem composed of bacteria, fungi, and viruses. Balance and integrity of the diverse microbes play an essential role in preventing pathogens from invading skin [
1], while the skin microbiome refers to the composition of all microbial genes in the skin’s community [
2]. Atopic dermatitis (AD), a worldwide heterogeneous, recurrent, chronic pruritic disease due to epithelial barrier dysfunction, immune dysregulation, and skin inflammation with dysbiosis of skin microbiota and colonization by the predominant pathogen
S. aureus, shows an increasing tendency [
3,
4]. Many studies have found alterations in the composition of the microbiome in patients with AD compared with that of healthy individuals, and microbiota differs between lesional skin and non-lesional skin [
5,
6]. AD can also affect the skin of any part of the body, but it generally shows age-related morphological and distributional characteristics [
7]. With the development of new technology, the application of whole genome sequencing (WGS) allows access to all genes of virtually all inflammation with dysbiosis of skin microbiota. Next-generation sequencing (NGS) technology in clinical bacteriology has been interrogating thousands of 16S ribosomal RNA gene amplicons from bacteria to archaea in floras from a patient with AD [
8,
9]. Currently, exploration of the skin microbiome in AD is attracting more and more attention from researchers. Dysbiosis in microbiota has been universally considered an important factor in the pathogenesis of AD, and how to achieve and maintain a balance between skin microbiota and the host has become a hot research topic in the field of AD treatment [
10]. Although traditional treatments including topical glucocorticoid and calcineurin inhibitors can inhibit inflammation, the recurrence of AD continues. Focusing on microbiota therapy is currently being developed to revise skin dysbiosis related to AD, with the expectation of obtaining long-term remission. In this review, we give a brief introduction on clinical features of AD, then discuss the pathogenesis of skin microbiota in AD, and finally discuss the treatment strategies based on the skin microbiome by reviewing literature published till October 2019. This article is based on previously conducted studies and does not contain any studies with human participants or animals performed by any of the authors.