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Garlic (Allium sativum L.) plays an important role in popular culture due to its dietary and medicinal uses. It is also used to produce a wide range of pharmacologically interesting molecules. Several pathogens affect garlic plants, especially Athelia (Sclerotium) rolfsii, a fungus that is widespread and causes large economic losses. It causes direct damage to crops and leads to plant stress, which induces secondary metabolite production in plants. The use of microorganisms as biocontrol agents may induce the production of beneficial metabolites in plants that will protect it and promote resistance to pathogen attack. In addition to suppressing disease, biological control agents may have elicitor effects that could induce an increase in the production of useful bioactive secondary metabolites in plants, some of which may be of pharmacological interest. Therefore, the search for new biological control agents should also consider their potential as elicitor agents. This paper presents an analysis of the biological control of Athelia (Sclerotium) rolfsii by antagonistic microrganisms, the potential of yeasts and bacteria of the genus Bacillus for the biocontrol of phytopathogens, microrganisms influence in nutritional and bioactive compounds content of interest to the pharmaceutical industry.