People with cystic fibrosis (CF) have chronic airway infection and frequent exposure to antibiotics, which often leads to the emergence of resistant organisms. In addition to the development of multiresistance in common CF pathogens such as Pseudomonas aeruginosa, several newer, inherently resistant gram-negative species are becoming more common, including Burkholderia cepacia complex, Stenotrophomonas maltophilia, Achromobacter (Alcaligenes) xylosoxidans, certain Ralstonia species, and those within the new genus Pandoraea. Many of these are closely related and have similar phenotypes, making accurate laboratory identification challenging. Although their role in contributing to pulmonary disease in CF is not clear, some, such as those of the B. cepacia complex, are clearly linked to an adverse prognosis, and both treatment and infection control issues can pose a real challenge.