Objective: To collect and identify the environmental bacteria in clean rooms, and to provide data for the investigation and analysis of the results of exceeding the standard, traceability analysis of drug-detecting bacteria and establishment and analysis of clean environmental bacteria database. Methods: Settling bacteria, plankton bacteria and surface microorganisms were collected in clean laboratories, operators and other monitoring points, and the identification and clarification were carried out by using the VITEK2 compact identification system. Results: A total of 53 bacterial isolations were identified from the controlled environment. The isolation ratios of Bacillus spp., Kocuria spp. and Staphylococcus spp. in total isolations were 17.0%, 15.1% and 13.2%, respectively after analysis of different cleanness levels and microbial species. Conclusion: Basic knowledge about the environmental microorganism composition in clean rooms was gained, and the database of environmental microbiology in clean rooms was preliminarily established. It is suggested that pharmaceutical enterprises should control the number of personnel in the clean areas, standardize the personnel's dressing procedures and clean area behavior, formulate effective cleaning and disinfection procedures, strengthen environmental monitoring, regularly analyze monitoring data, study datum trends and take measures in time to deal with abnormal data so as to keep the clean areas in a good state of control.