The karyotypes of five strains ofBotrytis cinerea were analysed by pulsed field gel electrophoresis (PFGE). None of the five chromosome patterns were identical and all five strains contained one or several minichromosomes of variable length. Considering that some of the chromosomal bands represent unresolved doublets, the total genome size of the five strains was estimated to vary between at least 33.9 and 39.7 megabasepairs (Mbp). Hybridization of blots of pulsed field gels with rDNA and s-tubulin probes revealed that these hybridize with the same chromosomal band. Chromosome-specific probes were isolated hybridizing to chromosomal bands 9 and 11 of strain SAS56. The latter two probes hybridized to only two of the five strains tested. The results are discussed in relation to the genome plasticity and variability of filamentous fungi.