Organic cultural relics such as Chinese paintings and calligraphy, ancient books, archives, textiles and lacquerware stored in museums often suffer from fungal contamination. In order to investigate fungal contamination of such cultural relics and to find effective methods to inhibit biodeterioration, we sampled, cultivated, isolated and identified fungi from some cultural relics and packaging boxes in four antique storerooms, using microscopic observation and molecular biological methods. Fourteen fungal strains were isolated from the cultural relic surfaces. Six genera, namely, Chaetomium, Malbranchea, Aspergillus, Peyronellaea, Comoclathris and Cladosporium, were identified by morphological observation and molecular biological methods. Chaetomium was the most prevalent, followed by Aspergillus. Most of these fungi can not only cause severe aesthetical damage to cultural relics, but also alter their material structures. Therefore, it is urgent that effective preventative and protective measures be taken. In this regard, the experimental results from this study could provide a scientific basis for related work in the future.