Due to the implementation of the Good Agricultural Practices (GAP) scheme, the verification of the microbiological safety of imported agricultural by-products used as mushroom substrates is now concerning. However, basic data on pathogenic fungi remain scarce. In this study, we examined fungal contamination levels (CFU/g) in the agricultural by-products imported in 2017 from Egypt, Germany, India, and Ukraine. Fungal loads ranged from 1.0 × 102 - 6.6 × 104 CFU/g. A total of 25 species across 10 genera were identified, including 21 species from Ascomycota, 3 species from Basidiomycota, and 1 species from Mucoromycota. Some of these species have been known to produce mycotoxins and exhibit pathogenicity toward humans or animals. The results of this study suggest that the fungal contamination in imported agricultural by-products is a critical factor to be considered in mushroom cultivation.