There are now four well-established methods to examine the chromosomes of filamentous fungi: mapping genes to linkage groups by recombination analyses, light-microscopic observation of chromosomes in meiotic divisions, electron-microscopic observation of the synaptonemal complexes between homologous chromosomes in prophase of meiosis, and separation of chromosomes as individual bands by pulsed field gel electrophoresis. These techniques and their contributions are described in brief with special reference toNeurospora. A fifth technique will be used more and more in characterizing chromosomes at the molecular level as DNA sequencing is completed for a limited number of the fungi. However, only the molecular studies of chromosome structures as they relate to centromeres, telomeres or nucleolus organizer regions are discussed, as is the potential usefulness of DNA sequencing to identify the junctions of chromosome rearrangements.