Stenotrophomonas maltophilia is a multi-drug resistant pathogen that has been isolated with increasing frequency from the hospitalized patients. A total of 202 S. maltophilia was isolated from three university hospitals and analysed by molecular typing for an epidemiologic investigation. All isolates were tested by antimicrobial susceptibility, random amplified polymorphic DNA (RAPD) analysis, and pulsed-field gel electrophoresis (PFGE). The RAPD and PFGE patterns were recorded and analysed by the unweighted-pair group method with arithmetic average method. Two or more isolates were considered to be clonally related if their PFGE pattern exhibited ${ge}80%$ similarity. Trimethoprim/sulfamethoxazole and ciprofloxacin were the most active antimicrobial agents tested. The majority of the isolates found to be genetically unrelated by PFGE. The genetically related isolates were recovered from the same patient. The result demonstrates a high genetic diversity of S. maltophilia isolates from clinical specimens. The clonal diversity of S. maltophilia from the hospitalized patients is partly due to the strains originated from the hospital environments, but not horizontal transfer between the patients.