Background: The present study was done to ascertain prevalence of Staphylococcus aureus from various canine affections in Banaskantha district of Gujarat, India. Along with this, use of classical and molecular techniques were compared in identification and virulence characterization of this pathogen.Methods: A total of 165 samples were collected and bacterial identification was carried out with bacteriological (phenotypic) techniques and confirmed by genus specific 16S rDNA and Staphylococcus aureus specific sa442 gene based PCR. Isolates were characterized for coagulase production, haemolysis activity and presence of spa gene. Result: Samples yielded, 88 (53.33%) Staphylococcus spp. via bacteriological and PCR methods. Clinically, 19 (21.59%), 28 (31.82%), 12 (13.64%), 15 (17.04%) and 14 (15.91%) isolates were from abscess/wound, pyoderma, respiratory problems, eye infections and Otitis, respectively. A total of 46/88 (52.27%) isolates were confirmed as Staphylococcus aureus in PCR. In tube coagulase test, 51/88 (57.95%) isolates were found positive. A tota of 42 isolates revealed presence of coa gene, including two tube coagulase negative isolates. Haemolytic activity revealed beta (51.14%) gamma (31.82%), alpha (13.64%) and alpha-beta (3.41%) haemolysis, respectively. X-region of Protein A (spa gene) was detected in 26 /46 (56.52%) isolates in PCR.