The occurrence of off-flavor problems caused by prokaryotes cyanobacteria and actinomycetes is a worldwide water and food quality issue. Based on literatures on two earthy-muddy-smelling metabolites, (i. e., geosmin and 2-methylisoborneol (2-MIB)), we reviewed their chemical characteristics, biosynthetic pathways, genes and enzymes that are involved in biosynthesis. Then we discussed current research questions related to off-flavor and future directions. Finally, we addressed the significance of probable key regulatory mechanism for the production and release of geosmin and 2-MIB, which could provide more scientific strategies to better control off-flavors outbreaks in drinking and aquaculture water.