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Staphylococcus aureus is a globally prevalent zoonotic pathogen frequently associated with pyoderma in humans, however, molecular data on primary staphylococcal pyoderma in Indian goats are meagre. This report presents the first molecular identification and phylogenetic analysis of S. aureus from a goat with primary pyoderma, along with clinical management. A four-month-old Malabari crossbred goat kid was presented to the Teaching Veterinary Clinical Complex, Mannuthy, with pustules and scab-like lesions on perianal and abdominal skin. Dermatological evaluation indicated primary pyoderma, and impression smears revealed Gram-positive cocci and neutrophils. The isolate was catalase positive and exhibited sensitivity to tetracycline, gentamicin, amoxicillin–sulbactam, ceftriaxone–tazobactam, and streptomycin, but showed resistance to multiple antibiotics. The isolate was identified as S. aureus by 16S rRNA gene sequencing. BLAST analysis revealed 99.48% sequence identity with S. aureus strains isolated from human cases of sepsis and pyoderma in Uzbekistan, India, and the USA, as well as with a complete genome sequence of a human blood isolate from Brazil.