Methicillin-resistant Staphylococcus aureus (MRSA) has become increasingly prevalent worldwide. Multi-resistant MRSA has been commonly reported to be one of the commonest causes of nosocomial infections worldwide. Also, recent reports describe MRSA in community. The aim of this study was to determine the prevalence of MRSA and their antimicrobial susceptibility pattern among hospital and community acquired Staphylococcus aureus isolates from Khartoum hospitals (Sudan), from September 2010 to September 2011. This is a cross sectional study. Staphylococcus aureus strains were isolated and identified from patients suffering from skin and wound infections in Khartoum using conventional microbiology techniques. MRSA strains were investigated by detection of mecA gene using PCR. MRSA strains were also tested for antimicrobial resistance using Kirby-Bauer NCCLS modified disc diffusion technique. A total of 223 strains of Staphylococcus aureus isolates were collected from 400 patients suffering wound and skin infections 46.2% (103/223) strains were from community acquired infections, and 53.8% (120/223) strains were from hospital acquired infections, 78 out of 223 (35.3%) were found to be methicillin resistant. Resistant to amoxyclav, cefepime, ciprofloxacin, gentamicin, tetracycline, rifampicin, vancomycin, erythromycin, clindamycin, and imipenem were found in 57.7%, 100%, 47.4%, 29.5%, 50%, 14.1%, 9%, 55.1%, 78.2%, and 3.8% MRSA strains respectively. Our study found high percentage MRSA strains. MRSA isolates showed resistance to at least two antibiotics tested while 64.1% were multi-drug resistant. Imipenem or vancomycin may be an alternative antibiotic for patients with wound or skin infection caused by MRSA.