Despite the wealth of knowledge available on the diversity of methicillin resistant Staphylococcus aureus (MRSA) strains that belonged to different clones, there have been no reports that analyzed such diversity on isolates belonging to the same clone. This study aimed to determine the diversity of ST239-MRSA strains, the predominant MRSA clone in worldwide, and to illustrate the correlation between the toxin genes, antimicrobial resistances and the genetic background of these strains. The molecular epidemiology of ST239-MRSA clone was analyzed by phenotypic antibiotyping, various genotypic assays. We found that coa-RFLP showed the highest discriminatory power in opposition to agr typing that had the lowest discriminatory power. The majority of our isolates (80%) were MDR, belonged to SCCmec III, agr I, coa genotype I and harbored sea and pvl genes. Our study demonstrated an overall negative correlation between the antimicrobial resistance and the toxin gene profiles. Meanwhile, there was no significant correlation between the toxin profiles and genetic background. The high diversity of ST239-MRSA strains might be among the contributors to the reported difficulties in control and prevention of MRSA infection in Egypt. With such diversity, it is assumed that these strains may have undergone different evolutionary processes.