Fungi are widely implicated in chronic rhinosinusitis. Direct microscopic examination (DME) is used to confirm the biological diagnosis of fungal rhinosinusitis (FRS). Diagnostic sensitivity of DME is better than culture, however DME does not allow fungal species identification. In this study, we included 54 sinus samples demonstrating hyphae on DME. Direct sequencing was compared to culture for the identification of the fungal species. Sequence analysis identified fungi in 81.5% of cases while culture was positive in only 31.5%. The most common genus was Aspergillus and the identified species belonged to section Fumigati or to section Flavi. Among other fungi identified by sequence analysis, Schizophyllum commune was present in three samples attesting to the importance of this Basidiomycetes in FRS. Our results clearly demonstrate the superiority of sequencing compared to culture when performed on specimens with hyphal elements at DME, and contributes to the epidemiological knowledge of fungi involved in FRS.