Abstract: Traditional methods for identification and classification of microorganisms have limitations in those of unculturable, slow-growth and special dietary needed bacteria. Fully automatic bacteria identification and drug susceptibility analysis system and MALDI-TOF MS are belonged to phenotype identification which is dependent obviously on the database of equipment. These two methods are defective in the variety kinds of environmental microorganisms. Modern molecular based identification methods supply new idea for the environmental microorganism analysis. 16S rRNA/ITS, a sequence contains conservative and variant region is not related with the culture state is widely used in the identification and classification of microorganisms. Microorganism is a significant factor for drug quality control. The present dissertation tried to explore the structure of 16S rRNA/ITS and its application on drug quality control area.