Objectives: Information is lacking on the methicillin-resistant Staphylococcus aureus (MRSA) clonal lineages circulating in Bolivia. We investigated the prevalence and molecular epidemiology of S. aureus colonization in hospitalized patients from the Bolivian Chaco, and compared their features with those of the few clinical isolates available from that setting. Methods: S. aureus nasal/inguinal colonization was investigated in 280 inpatients from eight hospitals in two point prevalence surveys (2012, n = 90; 2013, n = 190). Molecular characterization included genotyping (spa typing, multilocus sequence typing, and pulsed-field gel electrophoresis), detection of virulence genes, and SCCmec typing. Results: Forty-one inpatients (14.6%) were S. aureus nasal/inguinal carriers, of whom five were colonized by MRSA (1.8%). MRSA isolates mostly belonged to spa-type t701, harboured SCCmec IVc, and were negative for Panton–Valentine leukocidin (PVL) genes. However, a USA300-related isolate was also detected, which showed the characteristics of the USA300 Latin American variant (USA300-LV; i.e., ST8, spa-type t008, SCCmec IVc, presence of PVL genes, absence of arcA). Notably, all the available MRSA clinical isolates (n = 5, collected during 2011–2013) were also identified as USA300-LV. Conclusions: Overall, MRSA colonization in inpatients from the Bolivian Chaco was low. However, USA300-LV-related isolates were detected in colonization and infections, emphasizing the importance of implementing control measures to limit their further dissemination in this resource-limited area.