We analyzed distribution of toxin genes (sea-seo, eta, etb, tst, lukS/lukF-PV) among spa types and phage types of 39 Staphylococcus aureus (S. aureus) isolates from healthy and diseased animals. All isolates turned out to be mecA negative (MSSA). Nine spa types were identified: t144 and t723 (dogs), t084 (dogs and pigs), t5447 (cat), t1491 and t008 (pigs), t002, t127 and t3478 (poultry). Seven phage types were detected, enclosed within four phage groups: I (cat), II (dogs), III (pigs) and mixed group (dogs and pigs). Three poultry spa types proved to be non-typeable by phages. Toxin genes were detected in 33 out of the 39 animal isolates. Our analysis revealed that the incidence of some toxin genes in S. aureus is host specific. Canine isolates t144 of phage group II harbored exfoliative toxin gene (eta), and porcine isolates type t1491 representing phage group III showed enterotoxin A gene (sea). The enterotoxin gene cluster (egc1) and enterotoxin gene seh were found in non-typeable isolates from chicken and in one feline isolate type t5447.