The study profiled the skin bacterial microbiota in 111 Indonesian children aged 4–18 years with atopic dermatitis (AD) and 107 controls with non-atopic conditions, using swabs from AD lesions and control forearms. AD was diagnosed according to the Hanifin-Rajka criteria and the microbiota analyzed by 16S rRNA sequencing at the ASV level using DADA2, with diversity assessment and PERMANOVA. Children with AD were younger (mean 8.35 ± 3.51 years) than controls (9.91 ± 3.79 years, P=0.002) and most came from higher income families. Skin with AD lesions had significantly reduced alpha diversity, an overrepresentation of Staphylococcus aureus and Staphylococcus epidermidis, as well as the less frequent genera Acetobacter and Gluconobacter. PERMANOVA showed the effect of case-control status, family income, maternal atopy, maternal education and DNA concentration on microbial composition. Phylogenetic analysis revealed differences in Staphylococcus ASV at the genus level. The findings highlight distinct microbial profiles in higher-income tropical populations and the role of environmental and sociodemographic factors.