In modern agriculture, natural plant communities may be replaced by a single crop species. Weeds, some microorganisms, and viruses, as well as some herbivores are organisms that should be eliminated. Pesticides and fertilizers not only affect the pests and crops, but soil, non-pest species, water, food, and humans. In traditional agriculture weeds are components with an important ecological role in the maintenance of the system. Some weeds have been used as tools to control the growth of other weeds in traditional agroecosystems. Researchers on sustainable and organic agriculture get valuable information from traditional agriculture and currently are conducting research on plant breeding, soil fertility and tillage, crop protection, and cropping systems. Allelopathy and chemical ecology are directly involved in each of these fields and can play an important role in crop productivity, conservation of genetic diversity, and maintenance of ecosystems stability. Allelopathy has been shown to be related with problems of chemical interference between crops and weeds, crops and crops, toxicity of crops and weeds residues, and/or crops and weeds exudates. Problems of autotoxicity, orchard replanting, and forest regeneration are also referred as allelopathic. Allelopathy is strongly coupled with other stresses of the environment, including insects and disease, temperature extremes, nutrient and moisture variables, radiation, and herbicides. These stress conditions often enhance allelochemical production and increase the potential for allelopathic interference. Allelopathy offers potential for weed control through the production and release of allelochemicals from plants. Allelochemicals may impact the availability of nutrients through effects on the symbiotic microbes. Destruction and changes in the use of soils in the tropics have decreased biodiversity, bringing about the loss of valuable natural products. Many different types of useful products such as natural pesticides and drugs can arise from allelopathy studies. New methods must be generated for allelopathy as a part of the biotic resources management strategies.