Objective: To investigate the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) nasal carriage in rural and urban community settings of Bolivia and Peru. Methods: MRSA nasal carriage was investigated in 585 individuals living in rural and urban areas of Bolivia and Peru (one urban area, one small rural village, and two native communities, one of which was highly isolated). MRSA isolates were subjected to molecular analysis for the detection of virulence genes, characterization of the staphylococcal cassette chromosome mec (SCC. mec), and genotyping (multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE)). Results: An overall very low prevalence of MRSA nasal carriage was observed (0.5%), with MRSA carriers being detected only in a small rural village of the Bolivian Chaco. The three MRSA isolates showed the characteristics of community-associated MRSA (being susceptible to all non-beta-lactam antibiotics and harboring the SCC. mec type IV), were clonally related, and belonged to ST1649. Conclusions: This study provides an insight into the epidemiology of MRSA in community settings of Bolivia and Peru. Reliable, time-saving, and low-cost methods should be implemented to encourage continued surveillance of MRSA dissemination in resource-limited countries.