Phytotoxins are secondary microbial metabolites that play an essential role in the development of disease symptoms induced by fungi on host plants. Although phytotoxins can cause extensive-and in some cases devastating-damage to agricultural crops, they can also represent an important tool to develop natural herbicides when produced by fungi and plants to inhibit the growth and spread of weeds. An alternative strategy to biologically control parasitic plants is based on the use of plant and fungal metabolites, which stimulate seed germination in the absence of the host plant. Nontoxigenic fungi also produce bioactive metabolites with potential fungicide and insecticide activity, and could be applied for crop protection. All these metabolites represent important tools to develop eco-friendly pesticides. This review deals with the relationships between the biological activity of some phytotoxins, seed germination stimulants, fungicides and insecticides, and their stereochemistry.