Transverse alternating field electrophoresis (TAFE) was used to compare the electrophoretic karyotypes of seven Septoria tritici isolates sampled from a single population. Isolates were selected based on differences at 12 DNA restriction fragment length polymorphism (RFLP) loci. Significant differences in electrophoretic karyotype existed among the isolates. Isolates had 14–16 bands, believed to correspond to chromosomes, ranging in size from approximately 330 to 3500 kb. Homologous chromosomes were identified by hybridization of anonymous single-locus and multiplelocus nuclear DNA sequences to Southern blots of TAFE gels. Length differences of up to 20% existed among homologous chromosomes. Densitometry and probe hybridization data showed that several bands contained two chromosomes. Probe pSTS192 hybridized to two chromosomes in each isolate, supporting previous data which suggested that this probe hybridized to two unlinked RFLP loci. Hybridization with probe pSTL53 provided additional evidence of partial diploidy at an RFLP locus in one isolate.