Microorganisms such as fungi, bacteria and viruses produce a mixture of structurally related compounds referred to as secondary metabolites which have no function in their physiological development. The natural products of microbial origin are categorized into insecticides, fungicides, bactericides, herbicides and nematicides. The major insecticides of microbial origin include avermectins, milbemectins and spinosyns isolated from actinomycetes. Bacteria such as Bacillus thuringiensis and Photorhabdus luminescens are considered to be potential insecticides. Fungicides and bactericides from microbes comprise of strobilurins, blasticidin, kasugamycin, and validamycin among which, strobilurins are the new generation fungicides effective against both higher as well as lower fungi. Different species of Pseudomonas and Trichoderma have emerged as potential biocontrol agents for the major diseases of commercial crops. Hence, several beneficial microorganisms have been found to be the active ingredients of a new generation of microbial pesticides or the basis for many natural products of microbial origin.