Development of bacterial resistance to the antibiotics constituted a major health problem. Methicillin-Resistant Staphylococcus aureus (MRSA) is considered a prominent example. MRSA tends to develop resistance to multiple antibiotic classes rapidly. Furthermore, MRSA colonization was proven to be a major risk factor for infection and subsequent transmission. MRSA decolonization by nasal mupirocin application and chlorhexidine whole-body washing are now recommended. This study aimed to screen for the development of mupirocin and chlorhexidine resistance among MRSA isolated from health facilities that applied decolonization protocols. A total of 272 clinical staphylococcal isolates were investigated. 115 MRSA isolates were collected before application of any of decolonization protocols, 81 isolates were collected from the facilities that applied the targeted decolonization protocol and 76 isolates were collected from the facilities that applied universal decolonization protocol. The isolated strains were identified phenotypically and subjected to PCR for MRSA confirmation. The used PCR assay simultaneously enabled the identification of mupirocin and chlorhexidine resistance genes. The results showed that the baseline mupirocin resistance rate among MRSA isolates was considered moderate (13.9%). While, the baseline chlorhexidine resistance was rare (3.5%).The resistance prevalence rates for both agents did not change significantly during the decolonization practice. In conclusion, the application of the decolonization strategies did not result in a significant change in MRSA susceptibility to either mupirocin or chlorhexidine. However, these results should be interpreted with caution due the small sample size and the relative short period passed since stating the decolonization protocols.