Our investigation of indoor-housed cynomolgus macaques (Macaca fascicularis) by using automated identification followed by antibiotic susceptibility testing revealed 1 of 7 immunocompetent animals and 2 of 9 immunosuppressed monkeys as carriers of methicillin-resistant Staphylococcus aureus (MRSA). Follow-up management involving mupirocin treatment resulted in the conversion of the 3 MRSA carriers into MRSA-negative cases. Prospective assessment of newly imported monkeys involving 24-h culture of nasal swabs on chromogenic agar revealed that 22% (18 of 82 animals) were MRSA-positive. Mupirocin treatment successfully converted all of the MRSA-positive macaques into non-carriers, suggesting the feasibility of this simple, one-step screening procedure for rapidly identifying MRSA carriers in large cohorts. In addition, 8 animals that had been diagnosed MRSA-positive and subsequently treated with mupirocin demonstrated no recolonization during follow-up, even under immunosuppressive conditions. We propose rapid screening using chromogenic agar followed by mupirocin treatment as a time- and cost-effective regimen for managing MRSA in cynomolgus monkeys.