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The skin microbiota of atopic dermatitis (AD) patients is characterized by increased <i>Staphylococcus aureus</i> colonization, which exacerbates disease symptoms and has been linked to reduced bacterial diversity. Skin bacterial communities in AD patients have mostly been described at family and genus levels, while species-level characterization has been limited. In this study, we investigated the role of the bacteria belonging to the <i>Staphylococcus</i> genus using targeted sequencing of the <i>tuf</i> gene with genus-specific primers. We compared staphylococcal communities on lesional and non-lesional skin of AD patients, as well as AD patients with healthy controls, and determined the absolute abundance of bacteria present at each site. We observed that the staphylococcal community, bacterial alpha diversity, and bacterial densities were similar on lesional and non-lesional skin, whereas AD severity was associated with significant changes in staphylococcal composition. Increased <i>S. aureus</i>, <i>Staphylococcus capitis</i>, and <i>Staphylococcus lugdunensis</i> abundances were correlated with increased severity. Conversely, <i>Staphylococcus hominis</i> abundance was negatively correlated with severity. Furthermore, <i>S. hominis</i> relative abundance was reduced on AD skin compared to healthy skin. In conclusion, various staphylococcal species appear to be important for skin health.