Kabatiella caulivora is the causal agent of clover scorch, a fungal disease of clover (Trifolium) species. Variability within and between K. caulivora Race 1 and Race 2 was determined by cultural characteristics, isozymes, and amplified fragment length polymorphisms (AFLP). Cultural studies indicated isolates from both races were highly variable. No differences were identified within or between races by isozyme analysis. Similarity coefficients, determined from AFLP analysis, indicated that isolates from different races were often more similar than isolates from the same race. Comparison of single representative isolates from Race 1 and Race 2, collected at a Denmark (Western Australia) disease site, with isolates collected from another site of clover scorch outbreak at Esperance, 300 km east of Denmark, indicated most of the isolates causing the second outbreak were similar to Race 2, confirming previously conducted pathogenicity tests. It is hypothesised that Race 2 may have evolved from Race 1, and that the level of variability in the pathogen indicates the potential for development of further new races of K. caulivora. The requirement for improved selection strategies, including the screening of new cultivars and breeding lines with multiple isolates of the pathogen, is discussed in relation to these findings.