Atopic dermatitis (AD) is a chronic complex inflammatory skin disorder. AD characterized by multiple contributing factors, such as impairment in skin barrier integrity, participation of either innate or adaptive immunity arms, in addition to the pivotal roles of cutaneous microbiome. The analysis of cutaneous microbiota was performed using shotgun metagenomic sequencing on an Illumina HiSeq platform in parallel with 16s rRNA genes using MiSeq sequencing. Two samples for each sequencing technique were collected from one child and one adult subjects with AD. Metagenomic data from 16srRNA was in accordance with those from shotgun sequencing. Taxonomic profile of samples at genus level showed overrepresentation of Streptococcus in child and Staphylococcus in adults. Species level analysis of reads revealed monoclonality of Staphylococcus aureus community in comparison to heterogeneity of Staphylococcus epidermidis. 16S rRNA gene based analysis was unable to provide comprehensive description of bacterial communities, while shotgun metagenomic analyses described the composition of microbiota with high resolution at different taxonomic levels especially subspecies and single nucleotide variants levels. Finally, further studies using shotgun metagenomic approaches will be required for characterization of microbiome in healthy and diseased subjects.