Background: Community-associated meticillin-resistant . Staphylococcus aureus (CA-MRSA) was first reported in remote Australian Aboriginal communities. It is a prominent clinical pathogen in northern Australia with potential for transmission within the local hospital setting. Aim: To determine epidemiological characteristics of . S. aureus carriage within the Royal Darwin Hospital. Methods: We screened two patient groups: an 'admission group' recruited within 48 h of admission; and an 'inpatient group' recruited five or more days after admission. . S. aureus isolates were characterized by antibiotic susceptibility testing and genotyped by a multi-locus sequence type-based high-resolution melting scheme. Findings: S. aureus carriage on admission was 30.7% of 225 compared with 34.8% among 201 inpatients, with MRSA carriage of 2.2% and 18.9% respectively. We isolated CA-MRSA from 0.9% and 10.4%, and healthcare-associated (HCA)-MRSA from 1.3% and 9.0% of the admission and inpatient groups, respectively. Among the inpatient group, hospital-associated ST239 was the most common MRSA strain. CA-MRSA was represented by one clonal complex (CC) in the admission group (CC5) and seven CCs in the inpatient group (CC1, 93, 5, 6, 30, 75, 88). Conclusion: Inpatient carriage of multiple CA-MRSA lineages suggests selection for and transmission within the hospital of not only typical HCA-MRSA, but also diverse CA-MRSA strains.