Bordetella spp. are not normally included when considering the opportunistic bacterial species that are typically involved in respiratory tract infections in individuals with cystic fibrosis (CF). By using a combination of bacterial genotyping and 16S rDNA sequencing, Bordetella spp. were identified in cultures obtained from 43 individuals with CF. Most (n = 23) patients were infected with Bordetella bronchiseptica/parapertussis; five were infected with Bordetella hinzii, four with Bordetella petrii, three with Bordetella avium, and eight with unidentified Bordetella spp. Consideration should be given to the presence of these organisms in the evaluation of CF sputum cultures.