Staphylococcus is one of the most important pathogenic bacteria in chronic suppurative otitis media (CSOM). The prevalence of pathogenic bacteria in patients with CSOM has not been compared with the prevalence rates in patients from other fields of medicine. We investigated the pathogenic bacteria in CSOM throughout Korea and annual isolation rates of methicillin-resistant Staphylococcus aureus (MRSA) over 6 years. Routine culture results and susceptibility data of CSOM isolated from 2000 to 2005 were collected from six general hospitals in Korea, along with the results of all clinically isolated Staphylococci from one tertiary care teaching hospital. Of the 1,162 bacteria identified in 1,360 CSOM patients, 628 (54.0%) were Staphylococci in CSOM. Of the latter, 288 (45.9%) were MRSA, which accounted for 24.8% of identified bacteria. Of the 5,988 clinically isolated Staphylococci from one tertiary care hospital, 3,712 (61.9%) were MRSA. All MRSA isolated from CSOM patients were sensitive to vancomycin and teicoplanin, and 88.2% were sensitive to sulfamethoxazole/trimethoprim. In contrast, these strains showed little or no sensitivity to oxacillin, clindamycin, penicillin, and erythromycin. Annual MRSA isolation rates showed no tendencies to increase or decrease. MRSA was the most frequently identified Staphylococcus in patients with otorrhea. The isolation rate of MRSA has not changed over 6 years. Continuous and periodic surveillance of MRSA is necessary to reduce the spread of antibiotic-resistant pathogens and to guide appropriate antibacterial therapy.