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The goal of this research was to analyze the fungal community responsible for the biodeterioration of a pirogue in the National Maritime Museum of China and to make recommendations for the protection of this artifact. Molecular identification of fungal strains isolated from the surface of the pirogue and the air of the storage room that were most closely related to <i>Cladosporium</i>, <i>Penicillium</i>, <i>Talaromyces</i> and <i>Trichoderma</i> spp. DNA extracted from the samples was sequenced on the Illumina MiSeq platform. The results showed that the predominant fungal genera present were <i>Penicillium</i> sp., <i>Cladosporium</i> sp. and <i>Exophiala</i> sp. Thereafter, cellulose degradation experiments were carried out on the predominant fungi screened by pure culturing. Finally, we tested the sensitivity of the predominant fungal isolates to four biocides. This work suggests that we should pay more attention to <i>Penicillium</i> sp. and <i>Cladosporium</i> sp. in the protection of wooden artifacts, and environmental control is recommended as the main means of protecting the pirogue.