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Surface sterilization is generally used for isolating lichen-inhabiting fungi as well as endophytic fungi, and ethanol and sodium hypochlorite are commonly used as the sterilizer. However, there are few studies on whether the type of chemicals used for surface sterilization affects the isolation results of lichen-inhabiting fungi. In this study, the genus composition of the lichen-inhabiting fungi of two lichen species (Flavoparmelia caperata and Peltigera dilacerata) were investigated 1) to reveal how the isolation result changes before and after surface sterilization and 2) to examine the effect of the sterilizer (ethanol, sodium hypochlorite, or hydrogen peroxide) on the composition of the isolated fungi. We isolated 652 non-lichenized fungal isolates from the two-lichen species and identified 84 genera. It was found that 1) every sterilizer effectively removed the fungi on the lichen surface and that 2) the composition of isolated fungi varied depending on the type of surface sterilizer. It was also shown that, such as the genus Sarea , there were some lichen-inhabiting fungi which could not be isolated at all by surface sterilization with ethanol or sodium hypochlorite, which are commonly used. In addition, the genus Virgaria was detected as lichen-inhabiting fungi for the first time. Our results suggest that single surface sterilization alone may underestimate the genus composition of lichen-inhabiting fungi. • The genus composition of lichen-inhabiting fungi were investigated. • Three sterilizers were used individually for surface sterilization. • The genus composition of isolates varied depending on the type of surface sterilizer. • Single sterilization method may undervalue the diversity of lichen-inhabiting fungi. [ABSTRACT FROM AUTHOR]