The anterior nares are the major reservoir for Staphylococcus aureus in humans, where nasal carriage has a crucial function as a source for invasive infections. Despite various investigations on aerobic community members based on traditional cultivation methods, little is known on the overall microbial composition and complex in situ interactions, but such knowledge is highly warranted for effective S. aureus control strategies. As assessed using advanced culture-independent approaches, this study provides a comprehensive survey of the anterior nare bacterial community of 40 individuals. Previously undiscovered co-colonization patterns and natural variations in species composition were revealed and provide insights for future intervention strategies for the control of health-care- and community-associated S. aureus infections.