Black root rot is a seedling disease caused by the soilborne fungal pathogen Thielaviopsis basicola. It is a significant threat to cotton and other crops in Australia, especially in cooler areas and seasons. The pathogen, T. basicola, produces thick walled spores that can survive in the soil for years (Figure 1). Although it was first detected in NSW in the 1980s it quickly spread by movement of the spores attached to foot-ware or machinery wheels. In just over a decade it has come to affect more than half of the cotton farms in southern Queensland and New South Wales. Regular disease surveys of cotton fields in NSW have shown an increase of incidence from 22% of fields inspected in NSW in 1995 to over 60% of farms surveyed in NSW in the 2000/2001 season and it was estimated that the incidence of black root rot in 2004 have reached 95% of the fields regularly surveyed in northern NSW (Allen and Lonergan 1997; Allen 2002; Nehl and Allen 2001