Fusarium oxysporum is an important fungal pathogen of many crops. The genome of this pathogen has a "core" part and a highly dynamic lineage-specific part. Certain lineage specific chromosomes are determinants of host range. It has been shown previously that some chromosomes that are important for infection can be transferred between strains, and that some chromosomes were likely dispensable for normal growth and development.This work describes experiments that were designed to answer basic questions about core and lineage specific chromosomes, as well as the techniques that were developed to answer these questions. One question was to determine which chromosomes can be transferred and which can be lost. We determined which chromosomes are amenable for transfer by means of a screening method, which led to the discovery of transfer of core chromosomes which had not been previously described in any species of fungus.The stability during in-vitro growth of a number of chromosomes was tested by tagging chromosomes of interest with genes for fluorescent markers. A novel method of transformation employing flow cytometry to select transformants was developed to create the strains required for these experiments. Subsequent screening for loss of these fluorescent markers by means of flow cytometry led to the discovery of complete or partial loss of several chromosomes. This includes a chromosome which is part of the core genome as well as several lineage specific chromosomes. Surprisingly, large deletions in a chromosome known to be a determining factor of pathogenicity had little effect on pathogenicity.