Children with atopic dermatitis (AD) have a higher prevalence of Staphylococcus aureus colonization. Gentamicin is an important topical antibiotic that is used in the treatment of AD lesions. This study aimed to evaluate the prevalence of gentamicin resistance, Panton-Valentine Leukocidin (PVL), and Staphylococcal cassette chromosome mec (SCCmec) type in community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA), which colonizes the skin of the AD children. Gentamicin resistance in CA-MRSA isolates was detected using the E-test. Polymerase Chain Reaction (PCR) was used to test the genes for aminoglycoside modifying enzymes (AMEs), PVL, and SCCmec types of CA-MRSA isolates. A total of 29 isolates of CA-MRSA were obtained from the skin lesions of 100 patients, and a high prevalence of gentamicin resistance (79.3 %) was detected among these isolates. The most predominant AME gene among the gentamicin resistant isolates was aac(6′)-Ie-aph(2′)-Ia. However, the PVL gene was detected in 14 (48.3 %) of the isolates. Both gentamicin resistance and PVL were significantly associated with a high SCORAD score. SCCmec type V (31 %) was most common among the CA-MRSA isolates. This study revealed a high prevalence of gentamicin resistance among MRSA that colonises the skin of AD, with the aac(6′)-Ie-aph(2′)-Ia aminoglycoside-resistant determinant predominating. The most frequently observed cassette was SCCmec type V with the emergence of SCCmec type III among the MRSA colonizer strains.