Crop losses from weeds worldwide average 10% annually. Herbicide application is almost essential in modern agriculture to maintain high productivity. Increased awareness of the environmental damage caused by continued use of conventional synthetic herbicides has aroused great interest in biodegradable, selective and environmentally friendly herbicides. The increasing incidence of herbicide resistance in weeds has stimulated research for herbicidal compounds with new or novel sites and modes of action. Microbial metabolites have become the focus of attention of researchers searching for natural product alternatives to conventional herbicides. Two well-known commercial herbicides of microbial origin are anisomycin (commercial analogue, methoxyphenon) and bialaphos. Both were isolated from members of actinomycetes. Several phytotoxins have been isolated from microbial metabolites, e.g., herbicidins A and B, herbimycins A and B, nigericin, tentoxin and others. The list of microbial phytotoxins continues to M. increase. Actinomycetes are the major source of several herbicides and other bioactive compounds. The potential of discovering new phytotoxins from metabolites of microorganisms is still unlimited. Methods of isolation of actinomycetes, their screening for phytotoxins, separation of phytotoxins from metabolites and partial purification of the toxins are described. Included are screening of soil fungi for phytotoxin, mass culture of fungi, and bioassays.