Staphylococcus aureus isolates in 2001 from the nose and the throat of an adult population were characterized for their incidence and type. The incidence was 51%, present in 80 out of 157 individuals examined, consisting of 34 nasal carriers, 24 throat carriers, and 22 who carried the isolates in both the nose and throat. Among these isolates, 2 and 5 from the nose and the throat, respectively, were identified as methicillin-resistant S. aureus. S. aureus from the nose and throat of the same individuals were characterized for identification. Examination of their phenotypes revealed that in 11 individuals the clone of S. aureus in the throat was different from the nasal clone. These results suggested that staphylococcal flora in the nose and the throat were independently formed, and that attention should also be directed to the carriers of S. aureus in the throat for the control of nosocomial infection.