This study was undertaken to determine the prevalence of coagulase positive staphylococcus (CPS) in Jordan and to investigate the presence of genes encoding exfoliative toxins (eta, etb), and toxic shock syndrome toxin-1 (tst). Seven hundred and fifty three samples were used including 273 obtained from human sources and 480 from animals (sheep, cows, and goats). One hundred and sixty seven isolates were identified as CPS and appeared as gram positive cocci, non-motile, produced coagulase, catalase, reduce tellurite, were resistant to acriflavin, unable to produce oxidase and amylase. The prevalence of CPS colonizing human was 115(42.1%) with 26.0% in nasal and 16.0% in nails. Livestock-associated CPS was detected in 52(10.8%) of the samples. polymerase chain reaction (PCR) amplification revealed eta to be the most common toxin gene detected in 36.5 and 28.8%, followed by tst in 25.2 and 5.76% of human and animal isolates, respectively. The possession of various gene combinations was found in 15(8.98%) of the isolates including eta plus tst in 14(12.2%) and eta plus etb in 1(0.86%) of human isolates. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay was performed for all CPS by using TaqI restriction; the pattern revealed that 163(97.6%) were Staphylococcus aureus and were identified phenotypically and confirmed genotypically by amplification of kat gene, and 4(2.40%) identified as Staphylococcus pseudintermedius. Phylogenetic analysis indicated that clones characterized in this study were S. aureus subsp. aureus and S. pseudintermedius. Toxins genes are mostly prevalent among S. aureus subsp. aureus strains.