In this study, the fungus that has spread widely in Tanjiapo ruins museum of Changsha Tongguan kilnsites,Hunan province was quickly identified. The site was surveyed and the fungus that commonly pollutes archaeological sites was identified. Different typical of microbial samples were collected using a sterile scalpel, then the total genomic DNA was extracted, polymerase chain reaction (PCR) was used to amplify the fungal ITS regions. Through a search of a DNA library, the fungal groups were identified. The results indicated that Fusarium oxysporum,Phlebia brevispora, and Lyophyllum decastes were the major fungi polluting the surfaces of archaeological ruins in the study site. These fungi belong to families, Nectriaceae, Corticiaceae, and Lyophyllaceae respectively. All of them are saprophytic fungi, and are responsible for degradation of wood materials in the soil. Thereafter, it is concluded that a mass of root residues has provided vital nutrient sources for the aggressive proliferation of fungus, and the high temperature and relatively high humidity are major environmental factors that promote the explosion of fungal growth in this study site. The manual elimination of the fungi and of root debris, along with proper environmental controls, is encouraged for disease control in this archaeological museum.