Bacteria have produced many important secondary metabolites, especially in the pharmaceutical industry. However, the increase in the rediscovery rate of the known compound has been inconvenient to researchers and the pharmaceutical industry. Nevertheless, genome mining in bacteria has uncovered several cryptic metabolic pathways that may be key to discovering new secondary metabolites. The conventional laboratory environment, however, limits the metabolic pathways of microorganisms, making it impossible for secondary metabolites to be produced. As a result, researchers began using epigenetics to change the expression of the genes that code for secondary metabolites in microorganisms. Using epigenetics modifiers, secondary metabolite gene clusters are activated without altering the bacterial DNA sequence. This review article focuses on the different epigenetic changes and how they affect gene expression to activate the synthesis of secondary metabolites in bacteria.