OBJECTIVE To investigate the drug resistance of clinical isolates of Streptococcus pneumoniae and molecular epidemiology with BOX-PCR in Nanchang. METHODS Antibiotic susceptibility was determined by the Etest methods or K-B disk diffusion test. Twenty-nine Penicillin-resistant S. pneumoniae(PRSP) clinical isolates were molecularly typed by BOX-PCR to detect the clonal relationship of them. RESULTS 85.7% were resistant to erythromycin,57.1% were PRSP. The resistant rates to tetracycline,clindamycin,trimethoprim-sulfamethoxazole and chloramphenicol were 88.1%,79.8%,60.7%,and 28.6%. Amoxicillin/clavulanic acid,levofloxacin and ceftriaxone retained activity against most of the isolates. All of strains were susceptible to vancomycin. Twenty-nine S. pneumoniae strains were divided into 14 distinct types,and 19 subtypes with subtype A (n=4) as the predominant type. CONCLUSIONS The resistance rate of S. pneumoniae to penicillin is very high,BOX-PCR typing demonstrats a high discriminatory potential and easy to be accurately analyzed.