The Bupjusa and Seonamsa temples are located at places with geographically different condition, and therefore, differ with respect to building’s structure and layout. In addition, evident difference can be appeared by the regional climate. For the 2 years, we studied the concentration and diversity of the seasonal airborne fungi inside and outside of the 2 temples. In Seonamsa temple, airborne fungi concentration in the indoor and outdoor air was higher and the species diversity in the indoor air was lower, whereas, concentration variation was larger than that of Bupjusa temple. A total of 173 fungal isolates (including 54 genera) and 162 isolated (including 49 genera) were obtained from the indoor air of Bupjusa and Seonamsa temple, respectively. Whereas, 80 fungal isolates (including 33 genera) and 74 isolates (including 39 genera) were collected form the outdoor air of Bupjusa and Seonamsa temple, respectively. However, more fungal varieties were observed to be distributed inside Bupjusa and outside Seonamsa temples. Amongst all the fungi identified, ascomycetes were more dominant (plus or minus 90% points), followed by basidiomycetes and zygomycetes; which more presented in outdoor air than in indoor air. The airborne fungi concentration in spring (month of April) and autumn was higher than in any other season, for Seonamsa and Bupjusa temples, repectively. Genus Cladosporium was isolated from each site and season, with its dramatic increase noted in autumn. In addition, the highest basidiospore(s) number was obtained after the rain. Consequently, the results suggest that Seonamsa temple was more susceptible to biological damage than Bupjusa temple was.