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Bioaerosols are among the less studied particles in the environment. The lack of standardization in sampling procedures, difficulties related to the effect of sampling processes on the integrity of microorganisms, and challenges associated with the application of environmental microbiology analyses and molecular and culture methods frighten many young scientists. Every microorganism has its own particularities and acts differently when aerosolized in various conditions. Because the air is an extremely biologically diluted environment, it is necessary to concentrate its content before any analysis is performed. Challenges faced when applying molecular methods to air samples reveal the need for a better standardization of approaches for cell and nucleic acid recovery, the choice of genetic markers, and interpretation of data. This paper presents a few of the limits and difficulties tackled when molecular methods are …