A 2-step polymerase chain reaction (PCR) assay and random amplification of polymorphic DNA (RAPD) analysis, respectively, were assessed to identify coagulase-negative staphylococci organisms to the species level and to determine the strain diversity and spread of Staphylococcus epidermidis, the most frequently isolated species, in a medical center in Beirut, Lebanon. Our data indicated that PCR was faster and was more efficient in identifying S. epidermidis isolates than is conventional biochemical testing. RAPD analysis have shown that S. epidermidis strains were scattered across the different clinical services, demonstrating various clusters of infection in the medical center.