Phytotoxins refer to substances produced by plants or other organisms that are toxic to plants. Microorganisms are a lucrative source of phytotoxins. Several species of bacteria, actinomycetes, fungi and algae produce secondary metabolites and by-products of primary metabolic processes which have phytotoxic potential. Several strategies have been laid down for the discovery of these phytotoxic metabolites, which are of agricultural importance. There are different assay formats for the detection of microbial phytotoxins. Many microbial toxins have unique target sites with potential for exploitation by the herbicide industry. These toxins have different modes of phytotoxic action but a few of them shares molecular target sites with some conventional synthetic herbicides. As bio-rational eco-friendly agrochemicals, several host specific and non-host specific microbial phytotoxins are used either directly or as templates to control weed species. The production of microbial phytotoxins is sensitive to a number of diverse factors, which include composition and acidity of media and conditions of culturing etc. Some phytotoxins are isolated from microbes and showed potential bioactivity against various plant/weed species. Some microbial preparations are commercialized such as DeVine®, Collego®, and Dr. BioSedge® etc. while many others are patented. Besides the commercial production of microbial phytotoxins to be used as bioherbicides, different approaches are used to synthesize the analogues of existing bioactive molecules. But, microbial phytotoxins are unstable, have low spectrum of activity and less shelf-life. Despite of these limitations, the microbial phytotoxins may prove to be eco-friendly, non-toxic and selective bioherbicides to be used extensively in the near future as a complementary in integrated weed management systems.