Staphylococci are common residents of the nasal flora. As the nasal and oral cavities are anatomically joined at the pharynx, these organisms are generally believed to pass into the mouth consistently. Staphylococci are thus transient residents in the oral cavity. In our previous studies, although Staphylococcus epidermidis was most predominant in both nasal and oral cavities, the distribution of other Staphylococcus species showed diversity in the nasal and oral cavities. Our previous results indicate that the origins of nasal and oral staphylococci are not identical. To investigate the connection between staphylococci and the nasal and oral cavities, the homology of genotypes of Staphylococcus species using arbitrarily primed polymerase chain reaction (AP-PCR) was compared. Staphylococcus isolates from the nasal and oral cavities of the same subject showed different genotypes on AP-PCR using OPA-03 primer. These results indicate that staphylococci in the oral cavity are not derived from those in the nasal cavity, and do not move between the nasal and oral cavities.