Objectives. To study the epidemiology of Staphylococcus aureus skin and soft-tissue infections (SSTIs) in hospitalised children and adults in Gaborone, Botswana, and to describe the changes in antimicrobial susceptibilities of S. aureus isolates over time. Methods. A retrospective cohort study evaluated SSTI isolates from January 2000 to December 2007 at Princess Marina Hospital (PMH), a large tertiary referral centre in Gaborone. Eligible subjects were those hospitalised at PMH during the study period who had a skin or soft-tissue culture yielding a bacterial or fungal pathogen. The primary outcome measure was a skin or soft-tissue culture yielding S. aureus. Secondary outcomes were the organism’s antimicrobial susceptibilities. Results. S. aureus was detected in 857 (35.8%) of single-organism SSTI cultures, and 194 (22.6%) of these isolates were methicillin resistant (MRSA). The proportion of MRSA isolates increased over time (linear test of trend: p=0.03 from 2000 to 2003), and MRSA isolates were more likely than methicillin-susceptible isolates to be resistant to commonly used antimicrobials recommended by the national SSTI treatment guideline. Conclusions. We report a high and increasing proportion of MRSA SSTIs in Gaborone. This high rate of MRSA resistance to currently recommended empiric antibiotics for SSTIs dictates the need for revising national guidelines and ongoing prospective surveillance of SSTIs in this setting.