Weeds are a permanent component of anthropogenic ecosystems, which requires strict control to avoid the accumulation of their long–lasting seeds in the soil. With high crop infestation, many elements of crop production technologies (fertilization, productive varieties, growth stimulators, etc.) turn out to be practically meaningless due to high yield losses. Intensive use of chemical herbicides (CH) has led to undesirable consequences: contamination of soil and wastewater, accumulation of their residues in the crop, the emergence of CH-resistant populations of weeds. In this regard, the development of environmentally friendly CH with new mechanisms of action is relevant. Natural phytotoxins of plant or microbial origin may be directly explored in herbicidal formulations (biorational CH) or indirectly as scaffolds for nature-derived CH. This review considers: 1) the main current trends in the development of CH that may be important for enhancement of biorational herbicides; 2) advances in the development and practical application of natural compounds for weed control; 3) the use of phytotoxins as prototypes of synthetic herbicides. Some modern approaches such as computational methods of virtual screening and design herbicidal molecules, development of modern formulations, determination of molecular targets are stressed as important to make exploration of natural compounds more effective.