The chronic colonization of the lower airways by bacterial pathogens is the leading cause of morbidity and mortality in patients with cystic fibrosis (CF). Pseudomonas aeruginosa is the most common CF pathogen, followed by Staphylococcus aureus. Improvements in airway clearance and more effective treatment of the conventional CF pathogens has led to the emergence of new airway pathogens such as Stenotrophomonas maltophilia, Mycobacterium abscessus, and Achromobacter. More recently, it has become appreciated that the lower airways in patients with CF are colonized by a more complex polymicrobial community composed primarily of bacteria found in the upper respiratory tract. This includes obligate anaerobes, most commonly Prevotella. Expanded culturing methods and culture-independent molecular methods are being used to characterize the composition and dynamics of these polymicrobial communities in patients with CF. The contribution of the CF microbiome to airway disease is actively being investigated and will present new opportunities for disease management in CF. However, there remain many challenges that must be overcome if microbiome profiling is going to inform clinical practice.