Abstract:Fungus plays a significant role in biology-related domains and with the molecular biology technology advancing，the key step has necessitated the identification of fungus and transformant from molecular level. By far， however，there hasn't remained an ideal protocol for the massive strains identification.In the research，a device used for massive identification was designed， and a novel identification protocol mediated by PCR from molecular level， suitable for the device，was developed. In the article， through the cloning of genes encoding cellulase and relative regulatory factors which are located in genome of Trichoderma reesei， the cloning of promoter of phosphoglycerate kinase gene 1 and gene encoding xylanase，respectively located in genome and expression vector of S. cerevisiae and by ITS sequences cloning RAPD analasis of the two frequently -used strains mentioned above and strains Penicillium oxalicum， Rhizopus stolonifer， Aspergillus niger， Aspergillus carbonarius， Aspergillus japonicas. the protocol turned out to be an effective one with wide application potential， To a great degree，the establishment of the method has worked out the bottleneck of high-throughput molecular identification.