Background: Staphylococcus epidermidis is known as the most significant cause of nosocomial infections. Moreover, bloodstream infection is one of the noticeable and common infections in many wards of health care units, especially in intensive care units (ICU) and neonatal intensive care units (NICU). It has been proved that the mecA gene is the principal cause of methicillin resistance in Staphylococcus epidermidis strains. Also, mecA and other genes are located on staphylococcal cassette chromosome mec (SCCmec). Objectives: The aim of this study was investigating the genotypic characteristics of methicillin resistant Staphylococcus epidermidis (MRSE) strains isolated from hospitalized patients at the intensive care unit. Methods: A total of 121 isolates were recovered from bloodstream infections of ICU hospitalized patients in Al-Zahra hospital (Isfahan, Iran). Overall, fifty-three isolates belonged to S. epidermidis. Antibiotic susceptibility Test, determination of mecA gene, SCCmec types, Pulse Field Gel Electrophoresis (PFGE) and Multi-Locus Sequence Typing (MLST) methods were carried out as the preferential techniques. Results: In accordance to our study, 43.4% of isolates were resistant to cefoxitin, while the mecA gene was found in 25 (47.2%) isolates by the PCR method. In addition, various SCCmec types were detected from MRSE strains by using multiplex polymerase chain reaction (PCR). Furthermore, a total of 16 different pulsotypes were identified with PFGE typing via GelCompar II analysis. It is notable that the most prevalent ST type was ST2. Conclusions: Recognizing the source of infection is essential for monitoring the dissemination of infections, therefore this important issue is not acquired without various typing methods.