The chapter considers the existence of various microbial toxins in soil and various types of toxins that are present in soil and their detailed generation by microbes. Various phytotoxic substances are responsible for the hinderance in plant growth such as growth inhibitors and germination inhibitors. These toxins play a major role in producing negative impacts in stubble mulching. Various substances are released from plant parts and cause the plant to hinder in growth. It appears that under some chemical, physical and biological conditions it the field microbial toxins are produced and can accumulate those results in reduction of plant growth