The objective of this study was to determine the phenotypic methods that could differentiate coagulase positive S. aureus and coagulase negative S. aureus from other Staphylococci. Therefore, 35 (32.4%) Staphylococcal isolates were isolated out 108 different samples. Identification was performed using combined phenotypic and genotypic methods. Based on phenotypic identification, 15 isolates were coagulase positive Staphylococcal spp. (CPS) and 20 isolates were coagulase negative Staphylococcal spp. (CNS). Out of 15 CPS isolates, 10 (28.5%) isolates were acriflavine resistant and so identified as CPSA while out of 20 CNS isolates, 6(17.14%) isolates were also acriflavine resistant and so identified as CNSA.  Based on molecular identification, only 16/35isolates were found to be S. aureus. PCR confirmed the results of acriflavine sensitivity test where out of the 16 PCR confirmed S. aureus isolates, 10 isolates were typical coagulase positive S. aureus and 6 isolates were atypical coagulase negative S. aureus. By using PCR, the spa-X gene was detected in all S. aureus isolates while enterotoxin D gene was detected in only 2(33.3%) of atypical S. aureus isolates. Neither other enterotoxins (A, B, C) nor the pvl genes were detected in any isolate. Genotypic analysis revealed that both typical and atypical S. aureus isolates are virulent. In conclusion, attention must be paid toward accurate identification of atypical S. aureus as a cause of disease in human and animal. Acriflavine sensitivity test must be included in the scheme of phenotypic identification for accurate identification and differentiation of typical and atypical S. aureus from other Staphylococcal strains.