Cystic fibrosis (CF) patients become colonized by pathogenic bacteria as well as by
Candida
species. The interplay between different microorganisms may play a key role in the prognosis of CF. The aim of the study was to analyze the coexistence patterns of bacteria and
Candida
spp. in sputum samples of patients with CF and to compare these patterns with the results of patients with other respiratory disorders (ORD). Sputum samples from 130 patients with CF and 186 patients with ORD were cultured on six different agar plates promoting the growth of bacteria and yeasts. Bacterial and
Candida
species were identified with MALDI-TOF MS. Pathogenic bacteria were found in 69.2% of the sputum samples of the CF patients, and in 44.1% the patients with ORD. CF patients tended to have growth of
Pseudomonas aeruginosa
and
Staphylococcus aureus
in sputum more often than patients with ORD. Overall, there was no difference in the coexistence of pathogenic bacteria and
Candida
spp. in these patient groups. However, when analyzed at the species level,
P. aeruginosa
and
S. aureus
coexisted with
Candida
spp. more frequently in sputum samples of CF patients compared with patients with ORD. Also, when analyzed according to age, it was shown that the adult (≥ 18 years) CF patients had a higher rate of coexistence of any pathogenic bacteria and
Candida
spp. than the children with CF and the adult patients with ORD. The rate for colonization with
Candida
together with pathogenic bacteria is increased in adult patients with CF.