Abstract: Identification of RNA genetic fingerprint of four unknown strains was carried out in this study with Dupont Qualicon Riboprinter system, 16S rDNA sequence together with physiological and chemical characterizations was used as control.The results indicated both methods were effectively for four strains identification and the four strains were Escherichia coli, Streptococcus thermophilus, Bacillus licheniformis and Bacillus subtilis, respectively. RiboPrinter system was faster and more convenient, which could finish the identification in eight hours, while 16S rDNA sequencing and physiological and chemical characterizations determination were more economical and practical.Moreover, RiboPrinter system will lay the foundation for further typing and tracking on the basis of species identification.