Atopic dermatitis (AD) is a chronic inflammatory skin disorder that results in areas of dry, itchy skin. Several cultivation-dependent and -independent studies have identified changes in the composition of microbial communities in these affected areas over time and when compared to healthy control individuals. However, how these communities vary on affected and unaffected skin of the same individual, and how these communities respond to emollient treatment, remains poorly understood. Here we characterized the microbial communities associated with affected and unaffected skin of 49 patients with AD before and after emollient treatment using high-throughput sequencing of the 16S rRNA gene. We found that microbial diversity and community composition was different between affected and unaffected skin of AD patients prior to treatment. Differences were driven primarily by the overabundance of Staphylococcus species on affected skin and a corresponding decrease in bacterial diversity. After 84-days of emollient treatment, the clinical symptoms of AD improved in 72% of the study population. Microbial communities associated with affected skin of these treatment responders more closely resembled unaffected skin after treatment as indicated by increased overall diversity and a decrease in the abundance of Staphylococcus species. Interestingly, Stenotrophomonas species were significantly more abundant in the communities of 'responders', suggesting a possible role in restoration of the skin microbiome in patients with AD. We demonstrated that the comparison of affected and unaffected skin from the same individual provides deeper insight into the bacterial communities involved in the skin dysbiosis associated with AD. These data support the importance of emollients in the management of AD although future studies should explore how emollients and other treatments help to restore skin dysbioses.