Biocides (antiseptics and disinfectants) are widely used in hospitals and pharmaceutical industries for the contamination control. Emergence of reduced susceptibility to biocides is the major concern and this is caused by various factors, among which plasmid‐mediated resistance is common. Many publications describe the antibiotic resistance and mechanisms in clinical setting. However, there are only limited studies available in worldwide addressing the molecular mechanisms of biocide resistance in the pharmaceutical sector. In addition, there is a considerable lack of scientific reports regarding MIC values of typical biocides against pharmaceutical cleanroom environmental isolates. This review analyses the plasmid‐mediated resistance in typical pharmaceutical microorganisms and prevalence of biocides resistant genes among common clinical and pharmaceutical isolates. This review discusses the MIC values of biocides in pharmaceutical environmental isolates, indicating the importance of the correlation between presence or absence of biocide resistant genes and reduced susceptibility of MIC values. This review recommends that pharmaceutical organizations to adopt policies and test methodologies to examine the MICs of common cleanroom biocides against the most common types of cleanroom environmental isolates.