By using short single oligomer primer with arbitrarily chosen sequences in polymerase chain reaction, randomly amplified polymorphic DNA (RAPD) was applied in differentiating clinical isolates of 52 Klebsiella pneumoniae and 28 Staphylococcus aureus. RAPD produced multiple polymorphic DNA bands when K. pneumoniae DNA was used as template. Using DNA fingerprints technique, the similarity coefficients values of 52 K. pneumoniae was measured and calculated, and dendrogram was drawn. The 52 Klebsiella pneumoniae were divided into 7 Patterns. But in the 28 Staphylococcus aureus, 3 characteristic lands were obtained. Minor differences in the RAPD fingerprints were detected. The research findings demonstrated that RAPD has a potential as a widely useful tool in providing genotypic characters for taxonomic descriptions and molecular epidemiology study.