Chronic infection of Cystic Fibrosis (CF) airway can be caused by Fungi together with the known bacterial pathogens. The role and variability of fungal pathogens are not enough investigated. Commercially available assays on the base of molecular-genetics methods are elaborated mainly for the Candida and Aspergillus genera representatives. The goal of this investigation was the analyzing fungal pathogens of CF airway and the elaboration of the approach for identification of mycoses causative agents directly in respiratory samples of the patients. The specimens of CF patients and patients from intensive care units were examined. The method of the amplification and sequencing of principal DNA fragments was used. Literature study demonstrated that 34 genera of Actinomycota and Basidiomycota can infect CF airway. The comparative investigation of the candidate targets led to the conclusion that rRNA operon fragment, including Internal transcribed spacer (ITS) 1, 5.8S rRNA gene and ITS2 fulfilled all the requirements to the target for direct pathogens identification in the patient airway sample. The addition of genotyping scheme by the properly selected loci should enable to accelerate the identification of fungal pathogens' genotypes.