The disease black root rot (BRR) is caused by the soil born fungal pathogen Thielaviopsis basicola. This fungus has a broad host range, infecting 137 species, with a worldwide distribution (Honeess, 1994). The combination of a wide host range with the ability to produce persistent resting spores contributes to a high disease impact. BRR symptoms are readily identifiable in the field, with stunting of seedlings and characteristic black lesions on younger roots. While not killing the seedlings, except in extreme cases or in association with other seedling diseases, the stunting can carry through to maturity with significant yield reductions. in Australia BER is a relatively new disease, having only been found in cotton fields in 1989 (Allen, 1990), yet it has rapidly become a widespread major problem particularly when season temperatures are below average. Investigations are underway as a Cotton CRC project to assess the genetic diversity of the pathogen T.basicola. All understanding of the diversity is important for disease control measures to be instigated effectively; this includes plant breeding (even though resistance in cotton is yet to be found). The focus of this work is to examine the variation in Australia of strains of T.basicola, and from this information determine the pathogen's likely origins and effects on field outbreaks. To achieve this, molecular analysis of diversity will be combined with pathogenicity testing.