Eight strains of the mycoparasite Coniothyrium minitans were analysed for intraspecific variation by three different approaches: analysis of morpho-physiological characteristics; random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) analysis of the genomic DNA. A high variability in colony colour, gross morphology and conidial size was found depending on strain and culture conditions. All individual strains could be distinguished using the three type of analyses. However, a close correspondence between RAPD, AFLP patterns and morpho-physiological characteristics of C. minitans strains was not observed. Our results suggest AFLP analysis constituted a more efficient and reliable tool than RAPD analysis or morpho-physiological studies to detect intraspecific variability in C. minitans and to follow its fate after application in the field.