Black root rot (caused by Thielaviopsis basicola), is an important seedling pathogen in the cotton industry in Australia (Nehl et al. 2004). The disease develops in the early part of the season (3-5 weeks after sowing), under favourable weather conditions, especially low soil temperatures (16-20 DEGREES C). All production areas in NSW and Queensland currently have the pathogen. There are currently no practical eradication methods and prevention, by farm hygiene, is vital. The pathogen produces large quantities of thick-walled spores (chlamydospores) that persist in the soil over long periods. Movement of contaminated soil via farm machinery and vehicles has a significant contribution to transferring the pathogen within and between farms. Several leads are currently under investigation for developing better disease control, including the impact of crop rotations on spore concentration and disease, the use of novel biofumigation (green manure) crops, and the relationship between soil types and disease severity. A further avenue of research is the use of synthetic chemicals, such as acibenzolar-S-methyl (Bion, Syngenta Crop Protection), which act to induce resistance to the pathogen prior to the pathogen attacking the plant. This enhanced form of resistance is referred to as systemic acquired resistance (SAR).