At the Zhidanyuan Sluice Site of the Yuan Dynasty, the wooden components in the humid environment have been treated with 3-iodo-2-propynyl-butyl-carbamate (IPBC), a fungicide, for eight years. According to a survey in 2012, the total amount of bacteria and fungi were reduced by 89% and 56% in comparison with those recorded in 2007. However, the efficacy period of IPBC has been found to be shortened in recent years. Therefore, we reinvestigated fungal species on the wooden components and reevaluated antifungal effects of IPBC, in order to effectively arrest fungal growth on the water-saturated wooden components of the sluice site. In this study, eight high-abundance molds were isolated from the wooden components. The identification of the strains by morphological characteristics, culture characteristics and DNA-ITS sequence analysis shows that the species are significantly different from the previous ones. Widely distributed are an unclassified fungus and Trichoderma viride which have not been found at the site previously. The antifungal effects of IPBC on these fungi were tested using the method of filter paper fungistasis; the results show that the antifungal agents for wooden relics at the sluice site need to be updated.