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The fungal communities in mushroom compost phase Ⅱ was assessed using a combination of PCR amplification and sequencing of 18S rDNA from fungal isolates and nested PCR-TGGE analysis on the basis of DNA directly extracted from compost samples. The diversity of cultivated fungi isolated from compost samples was low. A total of 11 isolates were related to only 2 different species. One species, Chaetomium elatum, was identified within 10 isolates, and the other, with high similarity belonged to Penicillium expansum. The fungal flora associated with mushroom compost was then monitored with nested PCR-TGGE. The patts obtained revealed the more complex existence of fungal communities from the original compost samples than from thoses enriched with food waste and cow slurry.