Methicillin-resistant Staphylococcus aureus (MRSA) strains with inducible macrolide-lincosamide-streptogramin B (iMLS(B)) resistance phenotype may lead to clinical failure during clindamycin (CLI) therapy. The aim of this study was to determine the incidence of MLS(B) phenotypes by using D-test method and genotypes by using multiplex real-time PCR method in MRSA strains. A total of 265 MRSA strains were obtained from clinical samples from hospitalized and outpatients. Of the MRSA isolates, 225 (84.9%) were resistant to erythromycin (ERT), and 170 (64.1%) to CLI. Among the 225 ERT-resistant MRSA strains, the constitutive MLS(B) (cMLS(B)) rate was found in 49.3%, iMLS(B) in 39.1% and the M phenotype in 11.5%. Overall, ermA, ermC, ermA+ermC, msrA, ermC+msrA, and ermA+ermC+msrA genes were detected in 85 (37.7%), 60 (26.6%), 42 (18.6%), 26 (11.5%), 11 (4.8%), and 1 (0.4%) isolates, respectively. Most prevalent resistance determinant in MRSA strains was ermA, which was detected in 37.7% of the isolates. The 26 MRSA strains with M phenotype harboured only msrA gene. In conclusion, due to aware of the potential of CLI treatment failure, D-test should be performed and reported in MRSA strains in clinical laboratories. The multiplex real-time PCR method is easy to perform, fast and reliable method for the detection of MLS(B) resistance genotypes.