Identification and prevention of bio-deterioration by microorganisms in archaeological site is a big challenge for most archaeologists and conservators. Until recently, information about microbial bio-deterioration and bio-degradation at in-site archaeological and cultural relics excavation site has been quite limited.A cemetery of Xizhou dynasty in Dahekou, Yicheng, Shanxi province was used as an example, to explore techniques for rapidly detecting and possibly preventing microbial bio-deterioration in archaeological sites. After microscope examination at the locale followed by molecular biological identification in the laboratory, the dominant members of the fungal community that pollute the soil at the archaeological excavation site were identified. Most of the fungal belonged to the genera Pseudeurotium, Alternaria, and Plectosphaerella, their clones occuping about 23%、21% and 18%, respectively, of the entire clone library. The high temperature, relative high humidity, and the low atmosphere exchange rate in the vertical tomb are the main environmental factors causing the massive microbial pollution in the site. This study provides practical information regarding the collection of degrading microorganisms at archaeological excavation sites, and provides a theoretical basis for the prevention of such microbial prevention in the future.