An essential component of the plant body is the root system. It provides anchorage and support for the plant to explore its substrate, to absorb water and nutrients and to transport them above ground to the shoot system. Root systems are highly adaptive and responsive to environment flux (Stokes et al, 1996, Annals of Botany 78: 415-421).The root systems in cotton may vary in different cultivars, for example, cultivars infected with different soil-borne pathogens and cultivars with varying levels of disease resistance may show different root characteristics. The soil-borne black root rot and fusarium (Fov) wilt pathogens have been used in this project to determine whether different disease resistant lines show variations in their root architecture. The root architectures between different genotypes grown under normal conditions are also assessed in this project. More robust roots in cotton cultivars are of great agronomic significance in its potential to protect against cotton diseases without the need for chemicals. Cultivars showing robust root characteristics may be incorporated into new lines.It was found that cotton root architecture varies with genotype. Additionally, cotton cultivars respond to exposure to the pathogen Thielaviopsis basicola with some cultivars showing an increase in root branching and others showing a decrease. Furthermore, degree of root branching was seen to vary with relative resistance to the fusarium wilt pathogen