Black root rot caused by Thielaviopsis basicola has become a major seedling disease in cotton soils since 1989. The role of seedling pathogens has become increasingly evident in the establishment and early growth of cotton. It is now clear that seedling disease has complex aetiology, many potential pathogens and environmental factors contribute to reduced seedling growth and development. This project set out to examine two aspects with a view to reducing seedling disease: (1) develop measures of diversity of microbes in soils and correlate them with soil health esp in relation to seedling disease, and (2) determine the impact of land management and microbial diversity on the development of seedling disease, especially black root rot (BRR) which is caused by the fungus Thielaviopsis basicola.