Staphylococcus aureus is one of the most common cause of both community and healthcare-associated infections. As staphylococci have developed resistance to various antibiotics, initially to penicillins then to methicillin and glycopeptides and have the ability to cause epidemics, they continue to be a major problem from past to present. Methicillin resistance gave rise to the use of alternative antibiotics such as macrolides, however worldwide development of macrolide resistance limited the use of these antibiotics. Macrolide resistance occurs either through target site modification (MLS(B) phenotype, encoded by erm genes), efflux pumps (MS phenotype, encoded by msrA/B genes) or decreased cell wall permeability. The aim of this study was to investigate the MLS(B) resistance of clinical S.aureus strains with phenotypic and genotypic methods. A total of 404 S.aureus strains isolated from different clinical samples (50% wound, 15% tracheal aspirate and 35% other samples) of inpatients (93.3%) and outpatients (6.7%) were included in the study. Double disc synergy test (D-test) was used for the phenotypical research and PCR was used for the genotypical research of MLS(B) resistance of isolates. One hundred fifty eight (39.1%) of the S.aureus isolates were methicillin-resistant (MRSA), and 246 (60.9%) were methicillin-susceptible (MSSA). By the use of D-test, constitutive (cMLS(B)) and inducible (iMLS(B)) clindamycin resistance were detected in 19 and 111 isolates, respectively, while five isolates were MS phenotype and 268 isolates were S phenotype (susceptible to erythromycin and clindamycin). The resistance genes of 136 isolates with MLS(B) resistance phenotype were determined genotypically and among 111 isolates showing iMLS(B) phenotype ermA gene was found in 81.9% (83 MRSA, 8 MSSA), ermC gene in 10.8% (7 MRSA, 5 MSSA), msrA gene in 10.8% (11 MRSA, 1 MSSA), msrB gene in 1.8% (2 MRSA) and ermB gene in 0.9% (1 MRSA). Among 19 strains with cMLS(B) phenotype, ermA was found in 57.9% (10 MRSA, 1 MSSA), ermC in 36.8% (6 MRSA, 1 MSSA) and ermB in 15.8% (3 MRSA). Among five strains with MS phenotype, ermA was found in 80% (2 MRSA, 2 MSSA), msrA in 75% (3 MSSA), msrB in 50% (2 MSSA) and ermC in 25% (1 MSSA) of the isolates. ErmA and ermC genes were detected together in 14 isolates, ermA, ermC and msrA genes in one isolate, ermA and msrA genes in 11 isolates, ermA, msrA and msrB genes in three isolates and ermA and ermB genes in three isolates, respectively. In this study, two MRSA isolates with MS phenotype and negative D-test had only ermA gene and among two MSSA strains, erm genes were also determined in addition to msr genes. In our study RAPD-PCR method was used to investigate the clonal similarity, however no dominance of one or a number of clonal type was observed among the isolates in which the resistance genes were identified. In conclusion, the detection of MLS(B) resistance in S.aureus isolates is likely to influence the selection of antibiotics in the treatment of the infections caused by this bacteria.