In this study, the samples were taken by open dishe, swab and membrane filtration techniques from a company which manufactures pharmaceutical products in Turkey. Overall 255 bacterial strains were isolated from 112 samples; in manufacturing operators, dressing rooms, manufacturing areas, machines and equipments, water, microbiology laboratory and final products. Bacterial strains were identified according to their morphological and biochemical characteristics and 29 different bacterial species were determined. We found that 154 of the 255 isolated strains were coagulase negative Staphylococcus, 40 strains were Micrococcus, 44 strains were Bacillus and two strains were Corynebacterium. We also identified two Pseudomonas aeruginosa, two Burkholderia cepacia, one Staphylococcus aureus, Xanthomonas maltophilia, Aeromonas sabria, Ochrobactrum anthropi and Meeksella zoohelcum strains in the samples which were taken from the air of manufacturing areas, Pseudomonas chlororaphis, X.maltophilia, A.sabria and Agrobacter radiobacter from water samples and two A. radiobacter strains from final products. Using six different disinfectants which were routinely used at the pharmaceutical company, we assessed the inhibition coefficient, inferior lethal coefficient and superior lethal co-efficient against 29 strains of different species. For this purpose we used benzalkonium chloride, a combination of 9 % of benzalkonium chloride and nonionic surface active agent, a mixture of 5 % of benzalkonium chloride, 1,35 % of formaldehyde, 0,75 % of glutaraldehyde and 3,8 % of glyoxal, a mixture of 0.1% of glutaraldehyde, 32,5 % of 1-propanol and 18 % of ethanol, 10 % of sodium hypochloride and chloramine-T trihydrate. Consequently, the findings of our study showed that sodium hypochloride and chloramine- T trihydrate showed no activity against most of the strains at a concentration of 1/100, all the other disinfectants showed bactericidal activity and the combination of 9 % benzalkonium chloride and nonionic surface active agent was the most active disinfectant against the strains which were isolated from a pharmaceutical company.