Natural products involved in plant-plant and plant-microorganism ecological interaction (Allelochemicals) are an important potential source for alternative agrochemicals and pharmaceuticals, in order to solve the many problems derived from inadequate culture practices and abuse of synthetic herbicides. Isolation, structural determination, bioassay techniques and applicability for these compounds in crop protection and pharmaceutical research are discussed, and future trends on Allelochemicals applications are examined. The new strategies for sustainable ecosystems controlled by allelochemicals offer a particular interest for the development of human bases in space, since these products can stimulate or inhibit plant germination and growth, and permit to develop crops with low residue amounts in water, facilitating wastewater treatment and recycling.