Aims: To screen for the predominant bacteria strains distributed in clean rooms and to analyze their phylogenetic relationships. Methods and Results: The bacteria distributed in air, surfaces and personnel in clean rooms were routinely monitored using agar plates. Five isolates frequently isolated from the clean rooms of an aseptic pharmaceutical production workshop were selected based on their colony and cell morphology characteristics. Their physiological and biochemical properties, as well as partial 16S rDNA sequences, were analyzed. Results showed that all the five isolates belong to Gram positive bacteria, of which three were Staphylococcus, one Microbacterium and one Bacillus species. Sensitivity tests for these bacteria isolates to 3 disinfectants showed that isolate F03 was obtuse, and had low susceptivity to UV irradiation, while isolates F02, F01 and F04 were not sensitive to phenol treatment. Isolates F04, F01 and F05 were resistant to chlorhexidine gluconate. Conclusion: Bacteria widely distributed in clean rooms are mainly a group of Gram positive strains, showing high resistance to selected disinfectants. Significance and impact of the study: Clean rooms are essential in aseptic pharmaceutical and food production. Screening bacteria isolates and identifying them is part of good manufacturing practices, and will aid in finding a more effective disinfection method.