Indoor air quality is an essential aspect for occupational health including in a densely populated university. This study aimed to assess the indoor airborne microorganisms via biochemical and molecular approaches in five enclosed workplaces, and their resistance towards six commonly used antibiotics. Cfu/dm2/h for five enclosed workplaces was determined using settle plate technique with 1/1/1 scheme and Gram staining was performed for all pure strains isolated. Two strains with the highest count and with different morphologies were identified using biochemical test as well as 16S rRNA amplification and direct sequencing. Minimum inhibitory concentration for antibiotics was carried out for these two strains. In this study, 27 microbial strains with different morphologies were obtained from all workplaces and 2 strains with the highest count were strain J in café and strain M in library, which were identified as Bacillus cereus and Staphylococcus cohnii, respectively. Both of them were highly susceptible to ampicillin and tetracycline. With resistance up to 0.78 µg/mL; B. cereus was less sensitive to kanamycin and neomycin whereas S. cohnii was less sensitive to streptomycin. In conclusion, antibiotics resistant B. cereus and S. cohnii were two of the microorganisms showing the most abundance in the café and library of a Malaysian public university, respectively. This study may serve as the baseline for the prescriptions of antibiotics to airborne microbial related infections especially to the community in the university who seek for medical treatments; particularly for respiratory and digestive infections which often associated with indoor microenvironment.