Soil microorganisms are paramount in the biogeochemical cycling of both inorganic and organic nutrients in the soil and in the maintenance of soil quality. In particular, microbial activity in the rhizosphere is a major factor that determines the availability of nutrients to plants and has a significant influence on plant health and productivity. An understanding of the basic principles of rhizosphere microbial ecology, including the function and diversity of the microorganisms that reside there, is necessary before soil microbial technologies can be applied. AMF root colonization patterns in ten cotton cultivars were studied over a period. The efficiency of AMF and Trichoderma spp. on soil fertility, plant growth and health and the effect of fungicide seed dress on the introduced mycoflora, soil properties and plant health were assessed in two cotton cultivars for a period of 120 days after emergence. The ten cotton cultivars showed significant difference in mycorrhizal association. Wilt disease was controlled using Trichoderma and AMF, as well as soil quality was improved against the usage of chemical fungicides.