Cystic fibrosis (CF) is the most common, severe, autosomal recessive hereditary disease in Caucasians. That this disease causing gene encodes for a chloride channel in epithelial cells (CFTR, cystic fibrosis transmembrane conductance regulator). The resulting lung infection is the focus, because it is often life-limiting. Various circumstances lead to the development of anaerobic conditions in the mucus, so obligate anaerobes occur in virtually all patients. Drug therapy of CF consists of a daily replacement therapy and a therapy for exacerbations each with at least one antibiotic. The influence of antibiotics on the numerous occurring obligate anaerobes is still unclear. The resistance of obligate anaerobes to particular antibiotics are very high, but currently treatment is primarily against facultative anaerobes such as Pseudomonas aeruginosa. However, in the course of increasing antibiotic resistance occurring to obligate anaerobes may limit the therapeutic options significantly.