Medicinal and aromatic plants are important sources for plant secondary metabolites. The genetic manipulation of plants associated with in vitro plant regeneration systems facilitates efforts to engineer secondary product metabolic pathways. The fungal infections have been increasing in recent years due to several factors, namely, the increased incidence of high-risk patients, particularly immunocompromised hosts. Aromatic plants have been empirically used as antimicrobial agents, but the mechanisms of action are still unknown. Thyme has a great interest due to the possibility of its use in different applications, in medicine, in the cosmetic industry, or as food additives. Several studies have shown that thyme oils possess antimicrobial activity. Increasingly, plant breeding has taken advantage of molecular biology developments in order to genotype the species of interest to accelerate their selection. These approaches consist in choosing desired genotypes based on molecular markers or the knowledge of the genes involved in a particular trait. The in vitro culture techniques can be used to multiply plants selected after molecular and antifungal studies. The course of the investigation and the current state in relation to micropropagation, molecular studies, and antifungal action of the Thymus genus plants will be presented.