The emergence of hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) as a main cause of nosocomial infections is a global health problem. The present study was conducted to reveal the prevalence of MRSA in intensive care units (ICUs) based on biofilm formation ability and genetic diversity in agr and coa genes. A total of 85 MRSA isolates were analyzed by molecular typing of agr and coa genes from different clinical sources in ICUs using Multiplex PCR and PCR-RFLP methods, respectively. Biofilm formation of all MRSA isolates was investigated using phenotypic and genomic methods. Among 85 isolated MRSA, majority of isolates were belonged to agr type I (71.8%) followed by agr types II (7.1%). PCR-RFLP coa typing revealed 5 different coa types and 13 RFLP patterns. Meanwhile, 51.8% of isolates were strong biofilm formative which were among hospitalized patients 54.5%, and medical staff 75%. Additionally, among 85 MRSA isolates, 60 (70.6%) and 53 (62.4%) isolates had icaA and icaD genes respectively. Moreover 39 (45.9%) of MRSA isolates had both genes, while 11 (13%) isolates had no studied genes. Based on our findings there is no correlation between biofilm formation and the presence of specific types of the agr and coa genes among MRSA clinical isolates. In conclusion, genetic diversity in agr and coa types indicated the presence of various clones of MRSA in our studied ICUs. High prevalence of MRSA strains with agr type I and strong ability of biofilm formation could be most considered as necessity of performance effective infection control policy.